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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
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tree33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/mccall81_245T.html
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Start online docs of the development version
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<h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
@@ -151,120 +96,135 @@
extracts.</p>
</div>
- <pre class="usage"><span class='va'>mccall81_245T</span></pre>
-
-
- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div>
+ </div>
- <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
+ <div id="format">
+ <h2>Format</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
+ <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>
- <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+ <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 id="source">
+ <h2>Source</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
- doi: <a href='https://doi.org/10.1021/jf00103a026'>10.1021/jf00103a026</a></p>
+ <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'>&lt;-</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'>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>,
- phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>,
- anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span>
- <span class='va'>fit.1</span> <span class='op'>&lt;-</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'>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>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>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>
-</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
-#&gt; T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18
-#&gt; k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13
-#&gt; k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02
-#&gt; k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07
-#&gt; f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02
-#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02
-#&gt; sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05
-#&gt; Lower Upper
-#&gt; T245_0 99.246061385 1.084640e+02
-#&gt; k_T245 0.039631621 4.746194e-02
-#&gt; k_phenol 0.218013879 7.525762e-01
-#&gt; k_anisole 0.005370739 8.305299e-03
-#&gt; f_T245_to_phenol 0.547559081 6.924813e-01
-#&gt; f_phenol_to_anisole 0.000000000 1.000000e+00
-#&gt; sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $ff
-#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; T245 15.982025 53.09114
-#&gt; phenol 1.711229 5.68458
-#&gt; anisole 103.784093 344.76329
-#&gt; </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span>
- <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span>
- <span class='co'># the sink in the model generation</span>
- <span class='va'>SFO_SFO_SFO_2</span> <span class='op'>&lt;-</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'>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>,
- phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>,
- anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>fit.2</span> <span class='op'>&lt;-</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'>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>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>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>
-</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284
-#&gt; k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976
-#&gt; k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587
-#&gt; k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083
-#&gt; f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637
-#&gt; sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
-#&gt; Upper
-#&gt; T245_0 108.43904074
-#&gt; k_T245 0.04743877
-#&gt; k_phenol 0.75005585
-#&gt; k_anisole 0.00829550
-#&gt; f_T245_to_phenol 0.69212308
-#&gt; sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $ff
-#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; T245 15.982025 53.09114
-#&gt; phenol 1.711229 5.68458
-#&gt; anisole 103.784093 344.76329
-#&gt; </div><div class='input'> <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>
-</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">SFO_SFO_SFO</span> <span class="op">&lt;-</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">#&gt;</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">&lt;-</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">#&gt;</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">#&gt;</span> Estimate se_notrans t value Pr(&gt;t)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Lower Upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0 99.246061385 1.084640e+02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245 0.039631621 4.746194e-02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol 0.218013879 7.525762e-01</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole 0.005370739 8.305299e-03</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol 0.547559081 6.924813e-01</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_phenol_to_anisole 0.000000000 1.000000e+00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> $ff</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_phenol T245_sink phenol_anisole phenol_sink </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DT50 DT90</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245 15.982025 53.09114</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> phenol 1.711229 5.68458</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> anisole 103.784093 344.76329</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">&lt;-</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">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span> <span class="va">fit.2</span> <span class="op">&lt;-</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">#&gt;</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">#&gt;</span> Estimate se_notrans t value Pr(&gt;t) Lower</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0 108.43904074</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245 0.04743877</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol 0.75005585</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole 0.00829550</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol 0.69212308</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> $ff</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245_phenol T245_sink phenol_anisole phenol_sink </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DT50 DT90</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> T245 15.982025 53.09114</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> phenol 1.711229 5.68458</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> anisole 103.784093 344.76329</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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>
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