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Diffstat (limited to 'docs/articles/prebuilt')
72 files changed, 731 insertions, 700 deletions
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../../search.json" id="search-input" placeholder="Search for" autocomplete="off"> -</form> - - <ul class="navbar-nav"> -<li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> - + </div> </nav><div class="container template-article"> @@ -93,12 +78,13 @@ <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Testing hierarchical pathway kinetics with residue data on cyantraniliprole</h1> + + <h1>Testing hierarchical pathway kinetics with residue data on cyantraniliprole</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 16 November 2023</h4> + <h4 data-toc-skip class="date">Last change on 13 February +2023, last compiled on 12 Mai 2025</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="d-none name"><code>2022_cyan_pathway.rmd</code></div> @@ -117,7 +103,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.6 which is currently under +<p>The mkin package is used in version 1.2.10 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -1600,10 +1586,58 @@ sd(f_JCZ38_qlogis)</td> </tr> </tbody> </table> -<p>The model comparison below suggests that the pathway fits using DFOP +<p>The model comparisons below suggest that the pathway fits using DFOP or SFORB for the parent compound provide the best fit.</p> <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">sfo_path_1 const</td> +<td align="right">16</td> +<td align="right">2693.0</td> +<td align="right">2686.8</td> +<td align="right">-1330.5</td> +</tr> +<tr class="even"> +<td align="left">fomc_path_1 const</td> +<td align="right">18</td> +<td align="right">2427.9</td> +<td align="right">2420.9</td> +<td align="right">-1196.0</td> +</tr> +<tr class="odd"> +<td align="left">dfop_path_1 const</td> +<td align="right">20</td> +<td align="right">2403.2</td> +<td align="right">2395.4</td> +<td align="right">-1181.6</td> +</tr> +<tr class="even"> +<td align="left">sforb_path_1 const</td> +<td align="right">20</td> +<td align="right">2401.4</td> +<td align="right">2393.6</td> +<td align="right">-1180.7</td> +</tr> +<tr class="odd"> +<td align="left">hs_path_1 const</td> +<td align="right">20</td> +<td align="right">2427.2</td> +<td align="right">2419.4</td> +<td align="right">-1193.6</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left"></th> @@ -1656,20 +1690,13 @@ or SFORB for the parent compound provide the best fit.</p> <td align="right">-1180.7</td> </tr> <tr class="odd"> -<td align="left">hs_path_1 const</td> -<td align="right">20</td> -<td align="right">2427.2</td> -<td align="right">2419.4</td> -<td align="right">-1193.6</td> -</tr> -<tr class="even"> <td align="left">dfop_path_1 tc</td> <td align="right">20</td> <td align="right">2398.0</td> <td align="right">2390.1</td> <td align="right">-1179.0</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">sforb_path_1 tc</td> <td align="right">20</td> <td align="right">2399.9</td> @@ -1680,14 +1707,14 @@ or SFORB for the parent compound provide the best fit.</p> </table> <p>For these two parent model, successful fits are shown below. Plots of the fits with the other parent models are shown in the Appendix.</p> -<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[[</span><span class="st">"dfop_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="DFOP pathway fit with two-component error" width="700"><p class="caption"> DFOP pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png" alt="SFORB pathway fit with two-component error" width="700"><p class="caption"> @@ -1697,7 +1724,7 @@ SFORB pathway fit with two-component error <p>A closer graphical analysis of these Figures shows that the residues of transformation product JCZ38 in the soils Tama and Nambsheim observed at later time points are strongly and systematically underestimated.</p> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl_path_1</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level3"> @@ -1711,7 +1738,7 @@ corresponding amide (Addendum 2014, p. 109). As FOMC provided the best fit for the parent, and the biexponential models DFOP and SFORB provided the best initial pathway fits, these three parent models are used in the alternative pathway fits.</p> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">cyan_path_2</span> <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></span> <span> fomc_path_2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> <span> cyan <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"JCZ38"</span>, <span class="st">"J9Z38"</span><span class="op">)</span><span class="op">)</span>,</span> @@ -1789,7 +1816,7 @@ alternative pathway fits.</p> </table> <p>Using constant variance, separate fits converge with the exception of the fits to the Sassafras soil data.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_sep_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_sep_2_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_2_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> @@ -1831,11 +1858,11 @@ the fits to the Sassafras soil data.</p> <p>Using the two-component error model, all separate fits converge with the exception of the alternative pathway fit with DFOP used for the parent and the Sassafras dataset.</p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_saem_2</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mhmkin.html">mhmkin</a></span><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><span class="va">f_sep_2_const</span>, <span class="va">f_sep_2_tc</span><span class="op">)</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">cyan_saem_full</span><span class="op">[</span><span class="fl">2</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span><span class="op">)</span>,</span> <span> cluster <span class="op">=</span> <span class="va">cl_path_2</span><span class="op">)</span></span></code></pre></div> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> @@ -1862,8 +1889,9 @@ parent and the Sassafras dataset.</p> </tbody> </table> <p>The hierarchical fits for the alternative pathway completed -successfully.</p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +successfully, with the exception of the model using FOMC for the parent +compound and constant variance as the error model.</p> +<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> <colgroup> @@ -1894,11 +1922,12 @@ successfully.</p> </tr> </tbody> </table> -<p>In both fits, the random effects for the formation fractions for the -pathways from JCZ38 to JSE76, and for the reverse pathway from JSE76 to -JCZ38 are ill-defined.</p> -<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<p>In all biphasic fits (DFOP or SFORB for the parent compound), the +random effects for the formation fractions for the pathways from JCZ38 +to JSE76, and for the reverse pathway from JSE76 to JCZ38 are +ill-defined.</p> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left"></th> @@ -1916,27 +1945,54 @@ JCZ38 are ill-defined.</p> <td align="right">-1103.5</td> </tr> <tr class="even"> +<td align="left">dfop_path_2 tc</td> +<td align="right">22</td> +<td align="right">2234.4</td> +<td align="right">2225.8</td> +<td align="right">-1095.2</td> +</tr> +<tr class="odd"> +<td align="left">sforb_path_2 tc</td> +<td align="right">22</td> +<td align="right">2239.7</td> +<td align="right">2231.1</td> +<td align="right">-1097.9</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[</span><span class="fl">2</span><span class="op">:</span><span class="fl">3</span>,<span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> <td align="left">dfop_path_2 const</td> <td align="right">22</td> <td align="right">2288.4</td> <td align="right">2279.8</td> <td align="right">-1122.2</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">sforb_path_2 const</td> <td align="right">22</td> <td align="right">2283.3</td> <td align="right">2274.7</td> <td align="right">-1119.7</td> </tr> -<tr class="even"> +<tr class="odd"> <td align="left">dfop_path_2 tc</td> <td align="right">22</td> <td align="right">2234.4</td> <td align="right">2225.8</td> <td align="right">-1095.2</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">sforb_path_2 tc</td> <td align="right">22</td> <td align="right">2239.7</td> @@ -1951,21 +2007,21 @@ and BIC values and are plotted below. Compared with the original pathway, the AIC and BIC values indicate a large improvement. This is confirmed by the plots, which show that the metabolite JCZ38 is fitted much better with this model.</p> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"fomc_path_2"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png" alt="FOMC pathway fit with two-component error, alternative pathway" width="700"><p class="caption"> FOMC pathway fit with two-component error, alternative pathway </p> </div> -<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"dfop_path_2"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png" alt="DFOP pathway fit with two-component error, alternative pathway" width="700"><p class="caption"> DFOP pathway fit with two-component error, alternative pathway </p> </div> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"sforb_path_2"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-15-1.png" alt="SFORB pathway fit with two-component error, alternative pathway" width="700"><p class="caption"> @@ -1983,7 +2039,7 @@ created below that can be indexed by row and column indices, and which contains the degradation parameter names for which random effects should be excluded for each of the hierarchical fits contained in <code>f_saem_2</code>.</p> -<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">no_ranef</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><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><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">3</span>, ncol <span class="op">=</span> <span class="fl">2</span>, dimnames <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span><span class="op">)</span></span> <span><span class="va">no_ranef</span><span class="op">[[</span><span class="st">"fomc_path_2"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"log_beta"</span>, <span class="st">"f_JCZ38_qlogis"</span>, <span class="st">"f_JSE76_qlogis"</span><span class="op">)</span></span> <span><span class="va">no_ranef</span><span class="op">[[</span><span class="st">"fomc_path_2"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cyan_0"</span>, <span class="st">"f_JCZ38_qlogis"</span>, <span class="st">"f_JSE76_qlogis"</span><span class="op">)</span></span> @@ -1998,7 +2054,7 @@ be excluded for each of the hierarchical fits contained in <span><span class="va">f_saem_3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_2</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="va">no_ranef</span>,</span> <span> cluster <span class="op">=</span> <span class="va">cl_path_2</span><span class="op">)</span></span></code></pre></div> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_3</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> @@ -2028,7 +2084,7 @@ be excluded for each of the hierarchical fits contained in all updated fits completed successfully. However, the Fisher Information Matrix for the fixed effects (Fth) could not be inverted, so no confidence intervals for the optimised parameters are available.</p> -<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_3</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> @@ -2054,8 +2110,8 @@ confidence intervals for the optimised parameters are available.</p> </tr> </tbody> </table> -<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_3</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_3</span><span class="op">[</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left"></th> @@ -2073,27 +2129,54 @@ confidence intervals for the optimised parameters are available.</p> <td align="right">-1105.5</td> </tr> <tr class="even"> +<td align="left">dfop_path_2 tc</td> +<td align="right">20</td> +<td align="right">2237.3</td> +<td align="right">2229.5</td> +<td align="right">-1098.6</td> +</tr> +<tr class="odd"> +<td align="left">sforb_path_2 tc</td> +<td align="right">20</td> +<td align="right">2241.3</td> +<td align="right">2233.5</td> +<td align="right">-1100.7</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_3</span><span class="op">[</span><span class="fl">2</span><span class="op">:</span><span class="fl">3</span>,<span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> <td align="left">dfop_path_2 const</td> <td align="right">20</td> <td align="right">2282.2</td> <td align="right">2274.4</td> <td align="right">-1121.1</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">sforb_path_2 const</td> <td align="right">20</td> <td align="right">2279.7</td> <td align="right">2271.9</td> <td align="right">-1119.9</td> </tr> -<tr class="even"> +<tr class="odd"> <td align="left">dfop_path_2 tc</td> <td align="right">20</td> <td align="right">2237.3</td> <td align="right">2229.5</td> <td align="right">-1098.6</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">sforb_path_2 tc</td> <td align="right">20</td> <td align="right">2241.3</td> @@ -2106,7 +2189,7 @@ confidence intervals for the optimised parameters are available.</p> two-component error) are lower than in the previous fits with the alternative pathway, the practical value of these refined evaluations is limited as no confidence intervals are obtained.</p> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl_path_2</span><span class="op">)</span></span></code></pre></div> </div> </div> @@ -2134,21 +2217,21 @@ Agency are gratefully acknowledged.</p> <div class="section level3"> <h3 id="plots-of-fits-that-were-not-refined-further">Plots of fits that were not refined further<a class="anchor" aria-label="anchor" href="#plots-of-fits-that-were-not-refined-further"></a> </h3> -<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[[</span><span class="st">"sfo_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-20-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption"> SFO pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[[</span><span class="st">"fomc_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-21-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption"> FOMC pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_cyan_pathway_files/figure-html/unnamed-chunk-22-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption"> @@ -2166,11 +2249,11 @@ HS pathway fit with two-component error Hierarchical SFO path 1 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:27:41 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:35:03 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - k_cyan * cyan @@ -2183,7 +2266,7 @@ Data: Model predictions using solution type deSolve -Fitted in 421.347 s +Fitted in 445.08 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2294,11 +2377,11 @@ JSE76 143.91 478.04 Hierarchical SFO path 1 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:27:55 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:34:47 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - k_cyan * cyan @@ -2311,7 +2394,7 @@ Data: Model predictions using solution type deSolve -Fitted in 435.122 s +Fitted in 428.46 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2424,11 +2507,11 @@ JSE76 114.20 379.35 Hierarchical FOMC path 1 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:28:33 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:35:21 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2443,7 +2526,7 @@ Data: Model predictions using solution type deSolve -Fitted in 473.357 s +Fitted in 462.739 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2569,11 +2652,11 @@ JSE76 318.86 1059.22 NA Hierarchical FOMC path 1 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:28:46 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:35:31 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2588,7 +2671,7 @@ Data: Model predictions using solution type deSolve -Fitted in 486.031 s +Fitted in 472.067 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2707,11 +2790,11 @@ JSE76 210.98 700.9 NA Hierarchical DFOP path 1 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:29:15 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:36:02 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2730,7 +2813,7 @@ Data: Model predictions using solution type deSolve -Fitted in 514.477 s +Fitted in 503.671 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2853,11 +2936,11 @@ JSE76 200.41 665.76 NA NA NA Hierarchical DFOP path 1 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:31:58 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:38:54 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2876,7 +2959,7 @@ Data: Model predictions using solution type deSolve -Fitted in 677.928 s +Fitted in 674.81 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2999,11 +3082,11 @@ JSE76 179.30 595.62 NA NA NA Hierarchical SFORB path 1 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:29:33 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:36:26 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3021,7 +3104,7 @@ Data: Model predictions using solution type deSolve -Fitted in 532.937 s +Fitted in 527.639 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3164,11 +3247,11 @@ JSE76 193.42 642.53 NA NA NA Hierarchical SFORB path 1 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:31:58 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:38:31 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3186,7 +3269,7 @@ Data: Model predictions using solution type deSolve -Fitted in 677.936 s +Fitted in 651.67 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3329,11 +3412,11 @@ JSE76 177.11 588.3 NA NA NA Hierarchical HS path 1 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:29:18 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:36:13 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3348,7 +3431,7 @@ Data: Model predictions using solution type deSolve -Fitted in 518.128 s +Fitted in 514.353 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3475,11 +3558,11 @@ JSE76 187.01 621.23 NA NA NA Hierarchical FOMC path 2 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:40:28 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:47:30 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3494,7 +3577,7 @@ Data: Model predictions using solution type deSolve -Fitted in 499.317 s +Fitted in 505.533 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3543,28 +3626,28 @@ Likelihood computed by importance sampling 2249 2241 -1104 Optimised parameters: - est. lower upper -cyan_0 101.55265 9.920e+01 103.90593 -log_k_JCZ38 -2.32302 -2.832e+00 -1.81416 -log_k_J9Z38 -5.13082 -5.942e+00 -4.31990 -log_k_JSE76 -3.01756 -4.262e+00 -1.77360 -f_cyan_ilr_1 0.70850 3.657e-01 1.05135 -f_cyan_ilr_2 0.95775 2.612e-01 1.65432 -f_JCZ38_qlogis 3.86105 9.248e-01 6.79733 -f_JSE76_qlogis 7.51583 -1.120e+02 127.03921 -log_alpha -0.15308 -4.508e-01 0.14462 -log_beta 2.99165 2.711e+00 3.27202 -a.1 2.04034 1.811e+00 2.26968 -b.1 0.06924 5.745e-02 0.08104 -SD.log_k_JCZ38 0.50818 1.390e-01 0.87736 -SD.log_k_J9Z38 0.86597 2.652e-01 1.46671 -SD.log_k_JSE76 1.38092 4.864e-01 2.27541 -SD.f_cyan_ilr_1 0.38204 1.354e-01 0.62864 -SD.f_cyan_ilr_2 0.55129 7.198e-02 1.03060 -SD.f_JCZ38_qlogis 1.88457 1.710e-02 3.75205 -SD.f_JSE76_qlogis 2.64018 -2.450e+03 2455.27887 -SD.log_alpha 0.31860 1.047e-01 0.53249 -SD.log_beta 0.24195 1.273e-02 0.47117 + est. lower upper +cyan_0 101.55265 9.920e+01 103.9059 +log_k_JCZ38 -2.32302 -2.832e+00 -1.8142 +log_k_J9Z38 -5.13082 -5.942e+00 -4.3199 +log_k_JSE76 -3.01756 -4.262e+00 -1.7736 +f_cyan_ilr_1 0.70850 3.657e-01 1.0513 +f_cyan_ilr_2 0.95775 2.612e-01 1.6543 +f_JCZ38_qlogis 3.86105 9.248e-01 6.7973 +f_JSE76_qlogis 7.51583 -1.120e+02 127.0392 +log_alpha -0.15308 -4.508e-01 0.1446 +log_beta 2.99165 2.711e+00 3.2720 +a.1 2.04034 1.843e+00 2.2382 +b.1 0.06924 5.749e-02 0.0810 +SD.log_k_JCZ38 0.50818 1.390e-01 0.8774 +SD.log_k_J9Z38 0.86597 2.652e-01 1.4667 +SD.log_k_JSE76 1.38092 4.864e-01 2.2754 +SD.f_cyan_ilr_1 0.38204 1.354e-01 0.6286 +SD.f_cyan_ilr_2 0.55129 7.198e-02 1.0306 +SD.f_JCZ38_qlogis 1.88457 1.711e-02 3.7520 +SD.f_JSE76_qlogis 2.64018 -2.450e+03 2454.9447 +SD.log_alpha 0.31860 1.047e-01 0.5325 +SD.log_beta 0.24195 1.273e-02 0.4712 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 @@ -3595,15 +3678,15 @@ SD.log_k_J9Z38 0.8660 2.652e-01 1.4667 SD.log_k_JSE76 1.3809 4.864e-01 2.2754 SD.f_cyan_ilr_1 0.3820 1.354e-01 0.6286 SD.f_cyan_ilr_2 0.5513 7.198e-02 1.0306 -SD.f_JCZ38_qlogis 1.8846 1.710e-02 3.7520 -SD.f_JSE76_qlogis 2.6402 -2.450e+03 2455.2789 +SD.f_JCZ38_qlogis 1.8846 1.711e-02 3.7520 +SD.f_JSE76_qlogis 2.6402 -2.450e+03 2454.9447 SD.log_alpha 0.3186 1.047e-01 0.5325 SD.log_beta 0.2420 1.273e-02 0.4712 Variance model: - est. lower upper -a.1 2.04034 1.81101 2.26968 -b.1 0.06924 0.05745 0.08104 + est. lower upper +a.1 2.04034 1.84252 2.238 +b.1 0.06924 0.05749 0.081 Backtransformed parameters: est. lower upper @@ -3641,11 +3724,11 @@ JSE76 14.169 47.07 NA Hierarchical DFOP path 2 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:41:25 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:48:20 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3665,7 +3748,7 @@ Data: Model predictions using solution type deSolve -Fitted in 555.724 s +Fitted in 555.413 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3832,11 +3915,11 @@ JSE76 24.32 80.78 NA NA NA Hierarchical DFOP path 2 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:44:08 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:51:02 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3856,7 +3939,7 @@ Data: Model predictions using solution type deSolve -Fitted in 718.988 s +Fitted in 717.675 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3933,15 +4016,15 @@ f_JSE76_qlogis 4.54884 -7.25628 16.35395 log_k1 -2.38201 -2.51639 -2.24763 log_k2 -4.66741 -4.91865 -4.41617 g_qlogis -0.28446 -1.14192 0.57300 -a.1 2.05925 1.83267 2.28582 -b.1 0.06172 0.05076 0.07268 +a.1 2.05925 1.86481 2.25369 +b.1 0.06172 0.05062 0.07282 SD.log_k_JCZ38 0.81137 0.25296 1.36977 -SD.log_k_J9Z38 0.83542 0.25396 1.41689 +SD.log_k_J9Z38 0.83542 0.25395 1.41689 SD.log_k_JSE76 0.97903 0.30100 1.65707 SD.f_cyan_ilr_1 0.37878 0.13374 0.62382 SD.f_cyan_ilr_2 0.67274 0.10102 1.24446 -SD.f_JCZ38_qlogis 1.35327 -0.42361 3.13015 -SD.f_JSE76_qlogis 1.43956 -19.15140 22.03052 +SD.f_JCZ38_qlogis 1.35327 -0.42359 3.13012 +SD.f_JSE76_qlogis 1.43956 -19.14972 22.02884 SD.log_k2 0.25329 0.07521 0.43138 SD.g_qlogis 0.95167 0.35149 1.55184 @@ -3972,19 +4055,19 @@ g_qlogis -0.1656 -0.0928 Random effects: est. lower upper SD.log_k_JCZ38 0.8114 0.25296 1.3698 -SD.log_k_J9Z38 0.8354 0.25396 1.4169 +SD.log_k_J9Z38 0.8354 0.25395 1.4169 SD.log_k_JSE76 0.9790 0.30100 1.6571 SD.f_cyan_ilr_1 0.3788 0.13374 0.6238 SD.f_cyan_ilr_2 0.6727 0.10102 1.2445 -SD.f_JCZ38_qlogis 1.3533 -0.42361 3.1301 -SD.f_JSE76_qlogis 1.4396 -19.15140 22.0305 +SD.f_JCZ38_qlogis 1.3533 -0.42359 3.1301 +SD.f_JSE76_qlogis 1.4396 -19.14972 22.0288 SD.log_k2 0.2533 0.07521 0.4314 SD.g_qlogis 0.9517 0.35149 1.5518 Variance model: est. lower upper -a.1 2.05925 1.83267 2.28582 -b.1 0.06172 0.05076 0.07268 +a.1 2.05925 1.86481 2.25369 +b.1 0.06172 0.05062 0.07282 Backtransformed parameters: est. lower upper @@ -4023,11 +4106,11 @@ JSE76 17.96 59.66 NA NA NA Hierarchical SFORB path 2 fit with constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:41:22 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:48:15 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4045,7 +4128,7 @@ Data: Model predictions using solution type deSolve -Fitted in 553.276 s +Fitted in 550.772 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4219,11 +4302,11 @@ JSE76 14.287 47.46 NA NA NA Hierarchical SFORB path 2 fit with two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:44:02 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 20:50:59 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4241,7 +4324,7 @@ Data: Model predictions using solution type deSolve -Fitted in 713.14 s +Fitted in 714.48 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4320,17 +4403,17 @@ f_cyan_ilr_1 0.70640 3.562e-01 1.057e+00 f_cyan_ilr_2 1.42704 3.170e-01 2.537e+00 f_JCZ38_qlogis 2.84779 1.042e+00 4.654e+00 f_JSE76_qlogis 8.63674 -6.407e+02 6.580e+02 -a.1 2.07082 1.846e+00 2.296e+00 -b.1 0.06227 5.120e-02 7.334e-02 +a.1 2.07082 1.877e+00 2.265e+00 +b.1 0.06227 5.098e-02 7.355e-02 SD.log_k_cyan_free 0.49674 1.865e-01 8.069e-01 -SD.log_k_cyan_bound_free 0.28537 6.808e-02 5.027e-01 +SD.log_k_cyan_bound_free 0.28537 6.809e-02 5.027e-01 SD.log_k_JCZ38 0.74846 2.305e-01 1.266e+00 SD.log_k_J9Z38 0.86077 2.713e-01 1.450e+00 SD.log_k_JSE76 0.97613 3.030e-01 1.649e+00 SD.f_cyan_ilr_1 0.38994 1.382e-01 6.417e-01 SD.f_cyan_ilr_2 0.82869 3.917e-02 1.618e+00 -SD.f_JCZ38_qlogis 1.05000 -2.809e-02 2.128e+00 -SD.f_JSE76_qlogis 0.44681 -3.986e+05 3.986e+05 +SD.f_JCZ38_qlogis 1.05000 -2.808e-02 2.128e+00 +SD.f_JSE76_qlogis 0.44681 -3.985e+05 3.985e+05 Correlation: cyn_f_0 lg_k_c_ lg_k_cyn_f_ lg_k_cyn_b_ l__JCZ3 l__J9Z3 @@ -4359,19 +4442,19 @@ f_JSE76_qlogis 0.0064 0.0345 0.2015 -0.7058 Random effects: est. lower upper SD.log_k_cyan_free 0.4967 1.865e-01 8.069e-01 -SD.log_k_cyan_bound_free 0.2854 6.808e-02 5.027e-01 +SD.log_k_cyan_bound_free 0.2854 6.809e-02 5.027e-01 SD.log_k_JCZ38 0.7485 2.305e-01 1.266e+00 SD.log_k_J9Z38 0.8608 2.713e-01 1.450e+00 SD.log_k_JSE76 0.9761 3.030e-01 1.649e+00 SD.f_cyan_ilr_1 0.3899 1.382e-01 6.417e-01 SD.f_cyan_ilr_2 0.8287 3.917e-02 1.618e+00 -SD.f_JCZ38_qlogis 1.0500 -2.809e-02 2.128e+00 -SD.f_JSE76_qlogis 0.4468 -3.986e+05 3.986e+05 +SD.f_JCZ38_qlogis 1.0500 -2.808e-02 2.128e+00 +SD.f_JSE76_qlogis 0.4468 -3.985e+05 3.985e+05 Variance model: - est. lower upper -a.1 2.07082 1.8458 2.29588 -b.1 0.06227 0.0512 0.07334 + est. lower upper +a.1 2.07082 1.87680 2.26483 +b.1 0.06227 0.05098 0.07355 Backtransformed parameters: est. lower upper @@ -4420,11 +4503,11 @@ Hierarchical FOMC path 2 fit with reduced random effects, two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:57:07 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:04:10 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4439,7 +4522,7 @@ Data: Model predictions using solution type deSolve -Fitted in 776.732 s +Fitted in 786.038 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4488,26 +4571,26 @@ Likelihood computed by importance sampling 2249 2242 -1106 Optimised parameters: - est. lower upper -cyan_0 101.24524 NA NA -log_k_JCZ38 -2.85375 NA NA -log_k_J9Z38 -5.07729 NA NA -log_k_JSE76 -3.53511 NA NA -f_cyan_ilr_1 0.67478 NA NA -f_cyan_ilr_2 0.97152 NA NA -f_JCZ38_qlogis 213.48001 NA NA -f_JSE76_qlogis 2.02040 NA NA -log_alpha -0.11041 NA NA -log_beta 3.06575 NA NA -a.1 2.05279 1.82393 2.28166 -b.1 0.07116 0.05910 0.08322 -SD.log_k_JCZ38 1.21713 0.44160 1.99266 -SD.log_k_J9Z38 0.88268 0.27541 1.48995 -SD.log_k_JSE76 0.59452 0.15005 1.03898 -SD.f_cyan_ilr_1 0.35370 0.12409 0.58331 -SD.f_cyan_ilr_2 0.78186 0.18547 1.37824 -SD.log_alpha 0.27781 0.08168 0.47394 -SD.log_beta 0.32608 0.06490 0.58726 + est. lower upper +cyan_0 101.24524 NA NA +log_k_JCZ38 -2.85375 NA NA +log_k_J9Z38 -5.07729 NA NA +log_k_JSE76 -3.53511 NA NA +f_cyan_ilr_1 0.67478 NA NA +f_cyan_ilr_2 0.97152 NA NA +f_JCZ38_qlogis 213.48001 NA NA +f_JSE76_qlogis 2.02040 NA NA +log_alpha -0.11041 NA NA +log_beta 3.06575 NA NA +a.1 2.05279 1.85495 2.2506 +b.1 0.07116 0.05912 0.0832 +SD.log_k_JCZ38 1.21713 0.44160 1.9927 +SD.log_k_J9Z38 0.88268 0.27541 1.4900 +SD.log_k_JSE76 0.59452 0.15005 1.0390 +SD.f_cyan_ilr_1 0.35370 0.12409 0.5833 +SD.f_cyan_ilr_2 0.78186 0.18547 1.3782 +SD.log_alpha 0.27781 0.08168 0.4739 +SD.log_beta 0.32608 0.06490 0.5873 Correlation is not available @@ -4522,9 +4605,9 @@ SD.log_alpha 0.2778 0.08168 0.4739 SD.log_beta 0.3261 0.06490 0.5873 Variance model: - est. lower upper -a.1 2.05279 1.8239 2.28166 -b.1 0.07116 0.0591 0.08322 + est. lower upper +a.1 2.05279 1.85495 2.2506 +b.1 0.07116 0.05912 0.0832 Backtransformed parameters: est. lower upper @@ -4563,11 +4646,11 @@ Hierarchical DFOP path 2 fit with reduced random effects, constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:58:51 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:05:56 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4587,7 +4670,7 @@ Data: Model predictions using solution type deSolve -Fitted in 880.94 s +Fitted in 892.139 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4729,11 +4812,11 @@ Hierarchical DFOP path 2 fit with reduced random effects, two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:58:58 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:02 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4753,7 +4836,7 @@ Data: Model predictions using solution type deSolve -Fitted in 887.853 s +Fitted in 898.534 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4830,13 +4913,13 @@ f_JSE76_qlogis 414.80884 NA NA log_k1 -2.38601 NA NA log_k2 -4.63632 NA NA g_qlogis -0.33920 NA NA -a.1 2.10837 1.88051 2.33623 -b.1 0.06223 0.05108 0.07338 +a.1 2.10837 1.91261 2.30413 +b.1 0.06223 0.05085 0.07361 SD.log_k_JCZ38 1.30902 0.48128 2.13675 SD.log_k_J9Z38 0.83882 0.25790 1.41974 SD.log_k_JSE76 0.58104 0.14201 1.02008 SD.f_cyan_ilr_1 0.35421 0.12398 0.58443 -SD.f_cyan_ilr_2 0.79373 0.12007 1.46740 +SD.f_cyan_ilr_2 0.79373 0.12007 1.46739 SD.log_k2 0.27476 0.08557 0.46394 SD.g_qlogis 0.96170 0.35463 1.56878 @@ -4854,8 +4937,8 @@ SD.g_qlogis 0.9617 0.35463 1.5688 Variance model: est. lower upper -a.1 2.10837 1.88051 2.33623 -b.1 0.06223 0.05108 0.07338 +a.1 2.10837 1.91261 2.30413 +b.1 0.06223 0.05085 0.07361 Backtransformed parameters: est. lower upper @@ -4895,11 +4978,11 @@ Hierarchical SFORB path 2 fit with reduced random effects, constant variance </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:58:49 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:05:52 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4917,7 +5000,7 @@ Data: Model predictions using solution type deSolve -Fitted in 878.878 s +Fitted in 888.333 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5066,11 +5149,11 @@ Hierarchical SFORB path 2 fit with reduced random effects, two-component error </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:10 2023 -Date of summary: Thu Nov 16 04:59:11 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:21 2025 +Date of summary: Mon May 12 21:06:22 2025 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5088,7 +5171,7 @@ Data: Model predictions using solution type deSolve -Fitted in 899.539 s +Fitted in 916.619 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5167,8 +5250,8 @@ f_cyan_ilr_1 0.72263 NA NA f_cyan_ilr_2 1.45352 NA NA f_JCZ38_qlogis 2.00778 NA NA f_JSE76_qlogis 941.58570 NA NA -a.1 2.11130 1.88299 2.33960 -b.1 0.06299 0.05176 0.07421 +a.1 2.11130 1.91479 2.30780 +b.1 0.06299 0.05152 0.07445 SD.log_k_cyan_free 0.50098 0.18805 0.81390 SD.log_k_cyan_bound_free 0.31671 0.08467 0.54875 SD.log_k_JCZ38 1.25865 0.45932 2.05798 @@ -5182,7 +5265,7 @@ Correlation is not available Random effects: est. lower upper SD.log_k_cyan_free 0.5010 0.18805 0.8139 -SD.log_k_cyan_bound_free 0.3167 0.08467 0.5488 +SD.log_k_cyan_bound_free 0.3167 0.08467 0.5487 SD.log_k_JCZ38 1.2587 0.45932 2.0580 SD.log_k_J9Z38 0.8683 0.27222 1.4644 SD.log_k_JSE76 0.5933 0.14711 1.0394 @@ -5191,8 +5274,8 @@ SD.f_cyan_ilr_2 0.8854 0.13797 1.6329 Variance model: est. lower upper -a.1 2.11130 1.88299 2.33960 -b.1 0.06299 0.05176 0.07421 +a.1 2.11130 1.91479 2.30780 +b.1 0.06299 0.05152 0.07445 Backtransformed parameters: est. lower upper @@ -5237,13 +5320,13 @@ JSE76 25.44 84.51 NA NA NA <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.2 (2023-10-31) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.5.0 (2025-04-11) +Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -5261,56 +5344,52 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 +[1] rmarkdown_2.29 nvimcom_0.9-167 saemix_3.3 npde_3.5 +[5] knitr_1.49 mkin_1.2.10 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.2 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 -[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 -[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3 -[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 -[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 -[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 -[33] inline_0.3.19 tools_4.3.2 memoise_2.0.1 dplyr_1.1.2 -[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 -[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 -[45] MASS_7.3-60 ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 -[49] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 -[53] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 -[57] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 -[61] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 -[65] prettyunits_1.1.1 readxl_1.4.2 </code></pre> + [1] sass_0.4.9 generics_0.1.3 lattice_0.22-6 digest_0.6.37 + [5] magrittr_2.0.3 evaluate_1.0.3 grid_4.5.0 fastmap_1.2.0 + [9] cellranger_1.1.0 jsonlite_1.9.0 processx_3.8.6 pkgbuild_1.4.6 +[13] deSolve_1.40 mclust_6.1.1 ps_1.9.0 gridExtra_2.3 +[17] scales_1.3.0 codetools_0.2-20 textshaping_1.0.0 jquerylib_0.1.4 +[21] cli_3.6.4 rlang_1.1.5 munsell_0.5.1 cachem_1.1.0 +[25] yaml_2.3.10 inline_0.3.21 tools_4.5.0 dplyr_1.1.4 +[29] colorspace_2.1-1 ggplot2_3.5.1 vctrs_0.6.5 R6_2.6.1 +[33] zoo_1.8-13 lifecycle_1.0.4 fs_1.6.5 htmlwidgets_1.6.4 +[37] MASS_7.3-65 ragg_1.3.3 pkgconfig_2.0.3 desc_1.4.3 +[41] callr_3.7.6 pkgdown_2.1.1 pillar_1.10.1 bslib_0.9.0 +[45] gtable_0.3.6 glue_1.8.0 systemfonts_1.2.1 xfun_0.51 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.1 htmltools_0.5.8.1 +[53] nlme_3.1-168 compiler_4.5.0 readxl_1.4.4 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64927712 kB</code></pre> +<pre><code>MemTotal: 64927780 kB</code></pre> </div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </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></p> -<p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <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> diff --git a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png Binary files differindex b3d6066b..d2201974 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png +++ 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href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> - + </div> </nav><div class="container template-article"> @@ -93,12 +78,13 @@ <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</h1> + + <h1>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 16 November 2023</h4> +2023, last compiled on 12 Mai 2025</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small> <div class="d-none name"><code>2022_dmta_parent.rmd</code></div> @@ -116,7 +102,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.6. It contains the test data +<p>The mkin package is used in version 1.2.10. It contains the test data and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> @@ -1247,11 +1233,11 @@ Plot of the final NLHM DFOP fit <p>Finally, a summary report of the fit is produced.</p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div> -<pre><code>saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:35 2023 -Date of summary: Thu Nov 16 04:59:35 2023 +<pre><code>saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:46 2025 +Date of summary: Mon May 12 21:06:46 2025 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1263,7 +1249,7 @@ Data: Model predictions using solution type analytical -Fitted in 4.4 s +Fitted in 3.953 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1298,11 +1284,11 @@ DMTA_0 98.256267 96.286112 100.22642 k1 0.064037 0.033281 0.09479 k2 0.008469 0.006002 0.01094 g 0.954167 0.914460 0.99387 -a.1 1.061795 0.863943 1.25965 -b.1 0.029550 0.022529 0.03657 -SD.DMTA_0 2.068581 0.427706 3.70946 +a.1 1.061795 0.878608 1.24498 +b.1 0.029550 0.022593 0.03651 +SD.DMTA_0 2.068581 0.427178 3.70998 SD.k1 0.598285 0.258235 0.93833 -SD.g 1.016689 0.360057 1.67332 +SD.g 1.016689 0.360061 1.67332 Correlation: DMTA_0 k1 k2 @@ -1312,14 +1298,14 @@ g -0.0521 -0.0286 -0.2744 Random effects: est. lower upper -SD.DMTA_0 2.0686 0.4277 3.7095 +SD.DMTA_0 2.0686 0.4272 3.7100 SD.k1 0.5983 0.2582 0.9383 SD.g 1.0167 0.3601 1.6733 Variance model: est. lower upper -a.1 1.06180 0.86394 1.25965 -b.1 0.02955 0.02253 0.03657 +a.1 1.06180 0.87861 1.24498 +b.1 0.02955 0.02259 0.03651 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 @@ -1423,11 +1409,11 @@ Erythropoiesis.”</span> <em>BMC Bioinformatics</em> 22 (478). <a href="https:/ Hierarchical mkin fit of the SFO model with error model const </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:26 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:38 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1437,7 +1423,7 @@ Data: Model predictions using solution type analytical -Fitted in 0.788 s +Fitted in 0.793 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1495,11 +1481,11 @@ DMTA 12.24 40.65 Hierarchical mkin fit of the SFO model with error model tc </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:28 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:40 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1509,7 +1495,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.428 s +Fitted in 2.462 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1537,13 +1523,13 @@ Likelihood computed by importance sampling 798.3 797.1 -393.2 Optimised parameters: - est. lower upper -DMTA_0 97.271822 95.703157 98.84049 -k_DMTA 0.056638 0.029110 0.08417 -a.1 2.660081 2.230398 3.08976 -b.1 0.001665 -0.006911 0.01024 -SD.DMTA_0 1.545520 0.145035 2.94601 -SD.k_DMTA 0.606422 0.262274 0.95057 + est. lower upper +DMTA_0 97.271822 95.70316 98.84049 +k_DMTA 0.056638 0.02911 0.08417 +a.1 2.660081 2.27492 3.04525 +b.1 0.001665 -0.14451 0.14784 +SD.DMTA_0 1.545520 0.14301 2.94803 +SD.k_DMTA 0.606422 0.26227 0.95057 Correlation: DMTA_0 @@ -1551,13 +1537,13 @@ k_DMTA 0.0169 Random effects: est. lower upper -SD.DMTA_0 1.5455 0.1450 2.9460 +SD.DMTA_0 1.5455 0.1430 2.9480 SD.k_DMTA 0.6064 0.2623 0.9506 Variance model: - est. lower upper -a.1 2.660081 2.230398 3.08976 -b.1 0.001665 -0.006911 0.01024 + est. lower upper +a.1 2.660081 2.2749 3.0452 +b.1 0.001665 -0.1445 0.1478 Estimated disappearance times: DT50 DT90 @@ -1569,11 +1555,11 @@ DMTA 12.24 40.65 Hierarchical mkin fit of the FOMC model with error model const </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:27 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:39 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1583,7 +1569,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.28 s +Fitted in 1.408 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1646,11 +1632,11 @@ DMTA 11.41 42.53 12.8 Hierarchical mkin fit of the FOMC model with error model tc </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:28 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:40 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1660,7 +1646,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.793 s +Fitted in 2.735 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1693,11 +1679,11 @@ Optimised parameters: DMTA_0 99.10577 97.33296 100.87859 alpha 5.46260 2.52199 8.40321 beta 81.66080 30.46664 132.85497 -a.1 1.50219 1.23601 1.76836 -b.1 0.02893 0.02099 0.03687 -SD.DMTA_0 1.61887 -0.03636 3.27411 +a.1 1.50219 1.25801 1.74636 +b.1 0.02893 0.02048 0.03739 +SD.DMTA_0 1.61887 -0.03843 3.27618 SD.alpha 0.58145 0.17364 0.98925 -SD.beta 0.68205 0.21108 1.15303 +SD.beta 0.68205 0.21108 1.15302 Correlation: DMTA_0 alpha @@ -1706,14 +1692,14 @@ beta -0.1430 0.2467 Random effects: est. lower upper -SD.DMTA_0 1.6189 -0.03636 3.2741 +SD.DMTA_0 1.6189 -0.03843 3.2762 SD.alpha 0.5814 0.17364 0.9892 SD.beta 0.6821 0.21108 1.1530 Variance model: est. lower upper -a.1 1.50219 1.23601 1.76836 -b.1 0.02893 0.02099 0.03687 +a.1 1.50219 1.25801 1.74636 +b.1 0.02893 0.02048 0.03739 Estimated disappearance times: DT50 DT90 DT50back @@ -1725,11 +1711,11 @@ DMTA 11.05 42.81 12.89 Hierarchical mkin fit of the DFOP model with error model const </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:27 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:39 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1741,7 +1727,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.752 s +Fitted in 1.769 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1809,11 +1795,11 @@ DMTA 11.79 42.8 12.88 11.09 76.46 Hierarchical mkin fit of the DFOP model with error model tc </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:29 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:41 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1825,7 +1811,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.186 s +Fitted in 3.069 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1860,12 +1846,12 @@ DMTA_0 98.347470 96.380815 100.31413 k1 0.064524 0.034279 0.09477 k2 0.008304 0.005843 0.01076 g 0.952128 0.909578 0.99468 -a.1 1.068907 0.868694 1.26912 -b.1 0.029265 0.022262 0.03627 -SD.DMTA_0 2.065796 0.428485 3.70311 +a.1 1.068907 0.883665 1.25415 +b.1 0.029265 0.022318 0.03621 +SD.DMTA_0 2.065796 0.427951 3.70364 SD.k1 0.583703 0.251796 0.91561 -SD.k2 0.004167 -7.832168 7.84050 -SD.g 1.064450 0.397476 1.73142 +SD.k2 0.004167 -7.831228 7.83956 +SD.g 1.064450 0.397479 1.73142 Correlation: DMTA_0 k1 k2 @@ -1875,15 +1861,15 @@ g -0.0464 -0.0269 -0.2713 Random effects: est. lower upper -SD.DMTA_0 2.065796 0.4285 3.7031 +SD.DMTA_0 2.065796 0.4280 3.7036 SD.k1 0.583703 0.2518 0.9156 -SD.k2 0.004167 -7.8322 7.8405 +SD.k2 0.004167 -7.8312 7.8396 SD.g 1.064450 0.3975 1.7314 Variance model: est. lower upper -a.1 1.06891 0.86869 1.26912 -b.1 0.02927 0.02226 0.03627 +a.1 1.06891 0.88367 1.25415 +b.1 0.02927 0.02232 0.03621 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 @@ -1895,11 +1881,11 @@ DMTA 11.39 41.36 12.45 10.74 83.48 Hierarchical mkin fit of the HS model with error model const </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:28 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:39 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -1909,7 +1895,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.28 s +Fitted in 1.996 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1977,11 +1963,11 @@ DMTA 8.801 67.91 20.44 8.801 31.13 Hierarchical mkin fit of the HS model with error model tc </caption> <pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.2 -Date of fit: Thu Nov 16 04:59:29 2023 -Date of summary: Thu Nov 16 05:00:43 2023 +saemix version used for fitting: 3.3 +mkin version used for pre-fitting: 1.2.10 +R version used for fitting: 4.5.0 +Date of fit: Mon May 12 21:06:41 2025 +Date of summary: Mon May 12 21:07:51 2025 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -1991,7 +1977,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.658 s +Fitted in 3.389 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -2026,12 +2012,12 @@ DMTA_0 97.76571 95.81350 99.71791 k1 0.05855 0.03080 0.08630 k2 0.02337 0.01664 0.03010 tb 31.09638 29.38289 32.80987 -a.1 1.08835 0.88590 1.29080 -b.1 0.02964 0.02257 0.03671 -SD.DMTA_0 2.04877 0.42607 3.67147 +a.1 1.08835 0.90059 1.27611 +b.1 0.02964 0.02261 0.03667 +SD.DMTA_0 2.04877 0.42553 3.67200 SD.k1 0.59166 0.25621 0.92711 SD.k2 0.30698 0.09561 0.51835 -SD.tb 0.01274 -0.10914 0.13462 +SD.tb 0.01274 -0.10915 0.13464 Correlation: DMTA_0 k1 k2 @@ -2041,15 +2027,15 @@ tb -0.0668 -0.0103 -0.2013 Random effects: est. lower upper -SD.DMTA_0 2.04877 0.42607 3.6715 +SD.DMTA_0 2.04877 0.42553 3.6720 SD.k1 0.59166 0.25621 0.9271 SD.k2 0.30698 0.09561 0.5183 -SD.tb 0.01274 -0.10914 0.1346 +SD.tb 0.01274 -0.10915 0.1346 Variance model: est. lower upper -a.1 1.08835 0.88590 1.29080 -b.1 0.02964 0.02257 0.03671 +a.1 1.08835 0.90059 1.27611 +b.1 0.02964 0.02261 0.03667 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 @@ -2105,13 +2091,13 @@ Convergence plot for the NLHM HS fit with two-component error <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.2 (2023-10-31) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.5.0 (2025-04-11) +Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -2129,53 +2115,50 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 +[1] rmarkdown_2.29 nvimcom_0.9-167 saemix_3.3 npde_3.5 +[5] knitr_1.49 mkin_1.2.10 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.2 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 -[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 -[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 -[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.2 memoise_2.0.1 -[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 -[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 -[37] fs_1.6.2 MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 -[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 -[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 -[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 -[53] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 </code></pre> + [1] gtable_0.3.6 jsonlite_1.9.0 dplyr_1.1.4 compiler_4.5.0 + [5] tidyselect_1.2.1 gridExtra_2.3 jquerylib_0.1.4 systemfonts_1.2.1 + [9] scales_1.3.0 textshaping_1.0.0 yaml_2.3.10 fastmap_1.2.0 +[13] lattice_0.22-6 ggplot2_3.5.1 R6_2.6.1 generics_0.1.3 +[17] lmtest_0.9-40 MASS_7.3-65 htmlwidgets_1.6.4 tibble_3.2.1 +[21] desc_1.4.3 munsell_0.5.1 bslib_0.9.0 pillar_1.10.1 +[25] rlang_1.1.5 cachem_1.1.0 xfun_0.51 fs_1.6.5 +[29] sass_0.4.9 cli_3.6.4 pkgdown_2.1.1 magrittr_2.0.3 +[33] digest_0.6.37 grid_4.5.0 mclust_6.1.1 lifecycle_1.0.4 +[37] nlme_3.1-168 vctrs_0.6.5 evaluate_1.0.3 glue_1.8.0 +[41] codetools_0.2-20 ragg_1.3.3 zoo_1.8-13 colorspace_2.1-1 +[45] tools_4.5.0 pkgconfig_2.0.3 htmltools_0.5.8.1</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64927712 kB</code></pre> +<pre><code>MemTotal: 64927780 kB</code></pre> </div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </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></p> -<p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <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> diff --git a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png b/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png 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class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</h1> + + <h1>Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 16 November 2023</h4> +last compiled on 12 Mai 2025</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="d-none name"><code>2022_dmta_pathway.rmd</code></div> @@ -117,7 +103,7 @@ can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.6, which is currently under +<p>The mkin package is used in version 1.2.10, which is currently under development. It contains the test data, and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot @@ -1809,7 +1795,9 @@ performed on the basis of the refined fit shown above.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">saem_sforb_path_1_tc_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span>,</span> <span> n <span class="op">=</span> <span class="fl">32</span>, cores <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div> -<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<pre><code> + (subscript) logical subscript too long</code></pre> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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">saem_sforb_path_1_tc_reduced_multi</span><span class="op">)</span></span></code></pre></div> <pre><code><multistart> object with 32 fits: E OK @@ -1823,7 +1811,7 @@ the SAEM algorithm leads to parameter combinations for the degradation model that the numerical integration routine cannot cope with. Because of this variation of initial parameters, some of the model fits take up to two times more time than the original fit.</p> -<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mar <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">12.1</span>, <span class="fl">4.1</span>, <span class="fl">2.1</span>, <span class="fl">2.1</span><span class="op">)</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced_multi</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span>, las <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> @@ -1842,14 +1830,14 @@ ill-defined parameters.</p> </h2> <p>The SFORB pathway fits with full and reduced parameter distribution model are shown below.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-3-1.png" alt="SFORB pathway fit with two-component error" width="700"><p class="caption"> SFORB pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-4-1.png" alt="SFORB pathway fit with two-component error, reduced parameter model" width="700"><p class="caption"> @@ -1858,7 +1846,7 @@ SFORB pathway fit with two-component error, reduced parameter model </div> <p>Plots of the remaining fits and listings for all successful fits are shown in the Appendix.</p> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> @@ -1898,21 +1886,21 @@ Level with Nonlinear Mixed-Effects Models.”</span> <em>Environments</em> <div class="section level3"> <h3 id="plots-of-hierarchical-fits-not-selected-for-refinement">Plots of hierarchical fits not selected for refinement<a class="anchor" aria-label="anchor" href="#plots-of-hierarchical-fits-not-selected-for-refinement"></a> </h3> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sfo_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption"> SFO pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"fomc_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption"> FOMC pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption"> @@ -1938,13 +1926,13 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.2 (2023-10-31) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.5.0 (2025-04-11) +Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -1962,55 +1950,52 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 +[1] rmarkdown_2.29 nvimcom_0.9-167 saemix_3.3 npde_3.5 +[5] knitr_1.49 mkin_1.2.10 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.2 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3 -[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 -[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 -[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 -[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 -[33] tools_4.3.2 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 -[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 -[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 MASS_7.3-60 -[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 -[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 -[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 -[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 -[61] nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 prettyunits_1.1.1</code></pre> + [1] sass_0.4.9 generics_0.1.3 lattice_0.22-6 digest_0.6.37 + [5] magrittr_2.0.3 evaluate_1.0.3 grid_4.5.0 fastmap_1.2.0 + [9] jsonlite_1.9.0 processx_3.8.6 pkgbuild_1.4.6 deSolve_1.40 +[13] mclust_6.1.1 ps_1.9.0 gridExtra_2.3 scales_1.3.0 +[17] codetools_0.2-20 textshaping_1.0.0 jquerylib_0.1.4 cli_3.6.4 +[21] rlang_1.1.5 munsell_0.5.1 cachem_1.1.0 yaml_2.3.10 +[25] tools_4.5.0 inline_0.3.21 dplyr_1.1.4 colorspace_2.1-1 +[29] ggplot2_3.5.1 vctrs_0.6.5 R6_2.6.1 zoo_1.8-13 +[33] lifecycle_1.0.4 fs_1.6.5 htmlwidgets_1.6.4 MASS_7.3-65 +[37] ragg_1.3.3 pkgconfig_2.0.3 desc_1.4.3 callr_3.7.6 +[41] pkgdown_2.1.1 pillar_1.10.1 bslib_0.9.0 gtable_0.3.6 +[45] glue_1.8.0 systemfonts_1.2.1 xfun_0.51 tibble_3.2.1 +[49] lmtest_0.9-40 tidyselect_1.2.1 htmltools_0.5.8.1 nlme_3.1-168 +[53] compiler_4.5.0 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64927712 kB</code></pre> +<pre><code>MemTotal: 64927780 kB</code></pre> </div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </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></p> -<p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <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> diff --git a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png 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role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../../search.json" id="search-input" placeholder="Search for" autocomplete="off"> -</form> - - <ul class="navbar-nav"> -<li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> - + </div> </nav><div class="container template-article"> @@ -93,12 +78,13 @@ <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</h1> + + <h1>Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 4 August 2023, -last compiled on 16 November 2023</h4> +last compiled on 12 Mai 2025</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2023_mesotrione_parent.rmd" class="external-link"><code>vignettes/prebuilt/2023_mesotrione_parent.rmd</code></a></small> <div class="d-none name"><code>2023_mesotrione_parent.rmd</code></div> @@ -117,7 +103,7 @@ parameters. Because in some other case studies, the SFORB parameterisation of biexponential decline has shown some advantages over the DFOP parameterisation, SFORB was included in the list of tested models as well.</p> -<p>The mkin package is used in version 1.2.6, which is contains the +<p>The mkin package is used in version 1.2.10, which is contains the functions that were used for the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> @@ -1479,7 +1465,7 @@ according to the <code>illparms</code> function.</p> <tr class="odd"> <td align="left">HS</td> <td align="left"></td> -<td align="left"></td> +<td align="left">b.1</td> </tr> </tbody> </table> @@ -2439,13 +2425,13 @@ further refined to make them fully identifiable.</p> <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.2 (2023-10-31) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.5.0 (2025-04-11) +Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -2463,53 +2449,51 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 +[1] rmarkdown_2.29 nvimcom_0.9-167 saemix_3.3 npde_3.5 +[5] knitr_1.49 mkin_1.2.10 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.2 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 -[17] fansi_1.0.4 scales_1.2.1 textshaping_0.3.6 jquerylib_0.1.4 -[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 -[25] yaml_2.3.7 tools_4.3.2 memoise_2.0.1 dplyr_1.1.2 -[29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 -[33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 -[37] MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 -[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 -[45] glue_1.6.2 systemfonts_1.0.4 xfun_0.39 tibble_3.2.1 -[49] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-163 -[53] rmarkdown_2.21 compiler_4.3.2 </code></pre> + [1] gtable_0.3.6 jsonlite_1.9.0 dplyr_1.1.4 compiler_4.5.0 + [5] tidyselect_1.2.1 gridExtra_2.3 jquerylib_0.1.4 systemfonts_1.2.1 + [9] scales_1.3.0 textshaping_1.0.0 readxl_1.4.4 yaml_2.3.10 +[13] fastmap_1.2.0 lattice_0.22-6 ggplot2_3.5.1 R6_2.6.1 +[17] generics_0.1.3 lmtest_0.9-40 MASS_7.3-65 htmlwidgets_1.6.4 +[21] tibble_3.2.1 desc_1.4.3 munsell_0.5.1 bslib_0.9.0 +[25] pillar_1.10.1 rlang_1.1.5 cachem_1.1.0 xfun_0.51 +[29] fs_1.6.5 sass_0.4.9 cli_3.6.4 pkgdown_2.1.1 +[33] magrittr_2.0.3 digest_0.6.37 grid_4.5.0 mclust_6.1.1 +[37] lifecycle_1.0.4 nlme_3.1-168 vctrs_0.6.5 evaluate_1.0.3 +[41] glue_1.8.0 cellranger_1.1.0 codetools_0.2-20 ragg_1.3.3 +[45] zoo_1.8-13 colorspace_2.1-1 tools_4.5.0 pkgconfig_2.0.3 +[49] htmltools_0.5.8.1</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64928100 kB</code></pre> +<pre><code>MemTotal: 64927780 kB</code></pre> </div> </div> - 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