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@@ -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">|&gt;</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">|&gt;</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">|&gt;</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">&lt;-</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">&lt;-</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">|&gt;</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">&lt;-</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">|&gt;</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">|&gt;</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">|&gt;</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">|&gt;</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">|&gt;</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">&lt;-</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">&lt;-</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">&lt;-</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">&lt;-</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">|&gt;</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">|&gt;</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">|&gt;</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">|&gt;</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">|&gt;</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 &lt;= 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>
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+
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