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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <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> @@ -98,44 +41,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </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>Example datasets from the NAFTA SOP published 2015</h1> @@ -147,97 +92,107 @@ <p>Data taken from US EPA (2015), p. 19 and 23.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Appendix_B</span> - <span class='va'>NAFTA_SOP_Appendix_D</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Appendix_B</span></span> +<span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>2 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>a factor containing the name of the observed variable</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>time</code></dt> +<dd><p>a numeric vector containing time points</p></dd> - <p>2 datasets with observations on the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</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</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</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'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <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'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></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> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 -#> -#> Representative half-life: -#> [1] 841.41</div><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='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> + <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 id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></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_SOP_2015-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" 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