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</header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/dimethenamid_2018.R" class="external-link"><code>R/dimethenamid_2018.R</code></a></small> - <div class="hidden name"><code>dimethenamid_2018.Rd</code></div> + <h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/dimethenamid_2018.R" class="external-link"><code>R/dimethenamid_2018.R</code></a></small> + <div class="d-none name"><code>dimethenamid_2018.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and @@ -119,30 +79,31 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations.</p> </div> - <div id="ref-usage"> + <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">dimethenamid_2018</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <a href="mkindsg.html">mkindsg</a> object grouping seven datasets with some meta information</p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour Rev. 2 - November 2017 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The R code used to create this data object is installed with this package in the 'dataset_generation' directory. In the code, page numbers are given for specific pieces of information in the comments.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <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="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 7 mkinds objects</span> <span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 </span> @@ -203,11 +164,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># influence of ill-defined rate constants that have</span></span></span> <span class="r-in"><span><span class="co"># extremely small values:</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># If we disregards ill-defined rate constants, the results</span></span></span> <span class="r-in"><span><span class="co"># look more plausible, but the truth is likely to be in</span></span></span> <span class="r-in"><span><span class="co"># between these variants</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># We can also specify a default value for the failing</span></span></span> <span class="r-in"><span><span class="co"># log parameters, to mimic FOCUS guidance</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> @@ -221,11 +182,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># graphics device used)</span></span></span> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></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">f_dmta_saem_tc</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.5 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:28:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:28:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 16:58:17 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 16:58:17 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -238,7 +199,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 299.056 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 294.206 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -284,75 +245,75 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3192 83.8656 92.7729</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.0095</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.1550</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.4862 84.1127 92.8598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0512 -3.5674 -2.5351</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0576 -4.9013 -3.2139</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8584 -4.2572 -3.4595</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9779 -4.4844 -3.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1264 -0.2186 0.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1509 -0.2547 0.5565</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3891 -1.6962 -1.0819</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8307 1.0085</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1205 0.1549</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8167 8.0078</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0303 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0306 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0234 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0380 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0247 -0.0031 0.0022 0.0817 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0425 -0.0438 0.0319 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0216 -0.0267 -0.0890 -0.0349 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1805 -0.0136 0.0434 0.0791 0.0390 -0.0061 0.0053 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8167 8.0078</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.009</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.155</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8307 1.0085</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1205 0.1549</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.31924 83.865625 92.77286</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.48621 84.112654 92.85977</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04730 0.028230 0.07926</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01729 0.007437 0.04020</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02110 0.014162 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01872 0.011283 0.03107</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14551 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12169 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11062 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1461</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1455</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1217</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1106</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6222</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.68 48.76</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> -<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> -<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.68</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.09 133.17</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.85 109.11</span> +<span class="r-out co"><span class="r-pr">#></span> M31 37.02 122.97</span> <span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> <span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> <span class="r-in"><span><span class="co"># such random effects</span></span></span> @@ -364,27 +325,23 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></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="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<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> + </footer></div> + - - </body></html> |