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<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>
<a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
<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>
<a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
<a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
<a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
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<img src="" class="logo" alt=""><h1>Evaluate parent kinetics using the NAFTA guidance</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small>
<div class="d-none name"><code>nafta.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>The function fits the SFO, IORE and DFOP models using <code><a href="mmkin.html">mmkin</a></code>
and returns an object of class <code>nafta</code> that has methods for printing
and plotting.</p>
<p>Print nafta objects. The results for the three models are printed in the
order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</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">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for nafta</span></span>
<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="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>NAFTA (2011) Guidance for evaluating and calculating degradation
kinetics in environmental media. NAFTA Technical Working Group on
Pesticides
<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
accessed 2019-02-22</p>
<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
Calculate Representative Half-life Values and Characterizing Pesticide
Degradation
<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>ds</dt>
<dd><p>A dataframe that must contain one variable called "time" with the
time values specified by the <code>time</code> argument, one column called
"name" with the grouping of the observed values, and finally one column of
observed values called "value".</p></dd>
<dt>title</dt>
<dd><p>Optional title of the dataset</p></dd>
<dt>quiet</dt>
<dd><p>Should the evaluation text be shown?</p></dd>
<dt>...</dt>
<dd><p>Further arguments passed to <code><a href="mmkin.html">mmkin</a></code> (not for the
printing method).</p></dd>
<dt>x</dt>
<dd><p>An <code>nafta</code> object.</p></dd>
<dt>digits</dt>
<dd><p>Number of digits to be used for printing parameters and
dissipation times.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>An list of class <code>nafta</code>. The list element named "mmkin" is the
<code><a href="mmkin.html">mmkin</a></code> object containing the fits of the three models. The
list element named "title" contains the title of the dataset used. The
list element "data" contains the dataset used in the fits.</p>
</div>
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p>Johannes Ranke</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></span>
<span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span>
<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span>
<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span>
<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</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="va">nafta_evaluation</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span>
<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span>
<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Parameters:</span>
<span class="r-out co"><span class="r-pr">#></span> $SFO</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $IORE</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span>
<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span>
<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span>
<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span>
<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span>
<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> DTx values:</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span>
<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span>
<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</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="va">nafta_evaluation</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="nafta-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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