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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2023-10-30 17:09:21 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2023-10-30 17:09:21 +0100
commitb7901aac76df753ec1213cb02bebea055965ee87 (patch)
treee907e87d81aa07f19e8387acca612026337add75 /docs/articles/web_only
parent193b46af027c7b30abf7cf215d77517370e5fb2c (diff)
Update static docs
Diffstat (limited to 'docs/articles/web_only')
-rw-r--r--docs/articles/web_only/FOCUS_Z.html7
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-rw-r--r--docs/articles/web_only/benchmarks.html104
-rw-r--r--docs/articles/web_only/compiled_models.html31
-rw-r--r--docs/articles/web_only/dimethenamid_2018.html154
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-rw-r--r--docs/articles/web_only/saem_benchmarks.html85
37 files changed, 285 insertions, 110 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 4cda45e3..f19f59ad 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -134,7 +137,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 16 January 2018
-(rebuilt 2023-05-19)</h4>
+(rebuilt 2023-10-30)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_Z.rmd</code></div>
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index 98bc135b..be652d31 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
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index c1011a35..11c158fa 100644
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index 74173f36..4603d247 100644
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index 1c5793cc..1454c938 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
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index 98bc135b..be652d31 100644
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index 0380ba43..59524035 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
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index 87af8874..d87105fb 100644
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index 492cdcc8..06e3ff57 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
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diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 87cef18a..1c5be845 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -135,7 +138,7 @@ to the US EPA SOP for the NAFTA guidance</h1>
Ranke</h4>
<h4 data-toc-skip class="date">26 February 2019 (rebuilt
-2023-05-19)</h4>
+2023-10-30)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
<div class="hidden name"><code>NAFTA_examples.rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
index 1d4a25e0..de4a527f 100644
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diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 315ad54e..5d6fb6e2 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -134,7 +137,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-05-19)</h4>
+(rebuilt 2023-10-30)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
<div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -231,7 +234,15 @@ systems. All trademarks belong to their respective owners.</p>
</h3>
<p>Constant variance (t1) and two-component error model (t2) for four
models fitted to two datasets, i.e. eight fits for each test.</p>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="8%">
+<col width="54%">
+<col width="8%">
+<col width="12%">
+<col width="8%">
+<col width="9%">
+</colgroup>
<thead><tr class="header">
<th align="left">OS</th>
<th align="left">CPU</th>
@@ -433,6 +444,22 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
<td align="right">1.386</td>
<td align="right">1.960</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.5</td>
+<td align="right">2.369</td>
+<td align="right">3.632</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.6</td>
+<td align="right">2.856</td>
+<td align="right">4.960</td>
+</tr>
</tbody>
</table>
</div>
@@ -443,6 +470,15 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
by variable (t5) for three models fitted to one dataset, i.e. three fits
for each test.</p>
<table class="table">
+<colgroup>
+<col width="7%">
+<col width="50%">
+<col width="7%">
+<col width="11%">
+<col width="7%">
+<col width="8%">
+<col width="7%">
+</colgroup>
<thead><tr class="header">
<th align="left">OS</th>
<th align="left">CPU</th>
@@ -669,6 +705,24 @@ for each test.</p>
<td align="right">2.080</td>
<td align="right">1.106</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.5</td>
+<td align="right">1.823</td>
+<td align="right">5.555</td>
+<td align="right">2.404</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.6</td>
+<td align="right">1.761</td>
+<td align="right">5.405</td>
+<td align="right">2.462</td>
+</tr>
</tbody>
</table>
</div>
@@ -678,18 +732,18 @@ for each test.</p>
<p>Constant variance (t6 and t7), two-component error model (t8 and t9),
and variance by variable (t10 and t11) for one model fitted to one
dataset, i.e. one fit for each test.</p>
-<table class="table">
+<table style="width:100%;" class="table">
<colgroup>
+<col width="5%">
+<col width="40%">
+<col width="5%">
<col width="8%">
-<col width="19%">
-<col width="8%">
-<col width="12%">
-<col width="8%">
-<col width="8%">
-<col width="8%">
-<col width="9%">
-<col width="8%">
-<col width="9%">
+<col width="5%">
+<col width="5%">
+<col width="5%">
+<col width="6%">
+<col width="5%">
+<col width="6%">
</colgroup>
<thead><tr class="header">
<th align="left">OS</th>
@@ -992,6 +1046,30 @@ dataset, i.e. one fit for each test.</p>
<td align="right">0.712</td>
<td align="right">0.948</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.5</td>
+<td align="right">0.798</td>
+<td align="right">1.096</td>
+<td align="right">1.217</td>
+<td align="right">3.173</td>
+<td align="right">1.634</td>
+<td align="right">2.271</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">4.3.1</td>
+<td align="left">1.2.6</td>
+<td align="right">0.813</td>
+<td align="right">1.136</td>
+<td align="right">1.220</td>
+<td align="right">3.114</td>
+<td align="right">1.598</td>
+<td align="right">2.255</td>
+</tr>
</tbody>
</table>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 3c53b40a..1aa88e05 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -134,7 +137,7 @@ definitions in mkin</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
- <h4 data-toc-skip class="date">2023-05-19</h4>
+ <h4 data-toc-skip class="date">2023-10-30</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
<div class="hidden name"><code>compiled_models.rmd</code></div>
@@ -152,7 +155,7 @@ compiled from autogenerated C code when defining a model using mkinmod.
Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function
checks for presence of a compiler using</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>In previous versions, it used <code>Sys.which("gcc")</code> for this
check.</p>
<p>On Linux, you need to have the essential build tools like make and
@@ -213,10 +216,10 @@ solution is also implemented, which is included in the tests below.</p>
<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="st">"R package rbenchmark is not available"</span><span class="op">)</span></span>
<span><span class="op">}</span></span></code></pre></div>
<pre><code><span><span class="co">## test replications relative elapsed</span></span>
-<span><span class="co">## 4 analytical 1 1.000 0.099</span></span>
-<span><span class="co">## 3 deSolve, compiled 1 1.303 0.129</span></span>
-<span><span class="co">## 2 Eigenvalue based 1 1.697 0.168</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 21.475 2.126</span></span></code></pre>
+<span><span class="co">## 4 analytical 1 1.000 0.213</span></span>
+<span><span class="co">## 3 deSolve, compiled 1 1.418 0.302</span></span>
+<span><span class="co">## 2 Eigenvalue based 1 2.000 0.426</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 23.535 5.013</span></span></code></pre>
<p>We see that using the compiled model is by more than a factor of 10
faster than using deSolve without compiled code.</p>
</div>
@@ -247,15 +250,15 @@ compiled code is available.</p>
<span><span class="op">}</span></span></code></pre></div>
<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
<pre><code><span><span class="co">## test replications relative elapsed</span></span>
-<span><span class="co">## 2 deSolve, compiled 1 1.000 0.165</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 22.673 3.741</span></span></code></pre>
-<p>Here we get a performance benefit of a factor of 23 using the version
+<span><span class="co">## 2 deSolve, compiled 1 1.000 0.492</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 20.398 10.036</span></span></code></pre>
+<p>Here we get a performance benefit of a factor of 20 using the version
of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 1.2.4 on</p>
-<pre><code><span><span class="co">## R version 4.3.0 Patched (2023-05-18 r84448)</span></span>
+<p>This vignette was built with mkin 1.2.6 on</p>
+<pre><code><span><span class="co">## R version 4.3.1 (2023-06-16)</span></span>
<span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
-<span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre>
-<pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre>
+<span><span class="co">## Running under: Ubuntu 22.04.3 LTS</span></span></code></pre>
+<pre><code><span><span class="co">## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</span></span></code></pre>
</div>
</div>
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index a89631a2..1cffd561 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -135,7 +138,7 @@ from 2018</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change 1 July 2022,
-built on 19 May 2023</h4>
+built on 30 Oct 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small>
<div class="hidden name"><code>dimethenamid_2018.rmd</code></div>
@@ -222,12 +225,12 @@ least in some datasets the degradation slows down towards later time
points, and that the scatter of the residuals error is smaller for
smaller values (panel to the right):</p>
<div class="sourceCode" id="cb3"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p>
<p>Using biexponential decline (DFOP) results in a slightly more random
scatter of the residuals:</p>
<div class="sourceCode" id="cb4"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p>
<p>The population curve (bold line) in the above plot results from
taking the mean of the individual transformed parameters, i.e. of log k1
@@ -239,7 +242,7 @@ dominates the average. This is alleviated if only rate constants that
pass the t-test for significant difference from zero (on the
untransformed scale) are considered in the averaging:</p>
<div class="sourceCode" id="cb5"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p>
<p>While this is visually much more satisfactory, such an average
procedure could introduce a bias, as not all results from the individual
@@ -251,7 +254,7 @@ degradation model and the error model (see below).</p>
predicted residues is reduced by using the two-component error
model:</p>
<div class="sourceCode" id="cb6"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p>
<p>However, note that in the case of using this error model, the fits to
the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by
@@ -263,7 +266,7 @@ Status of individual fits:
dataset
model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot
- DFOP OK OK C OK C OK
+ DFOP OK OK OK OK C OK
C: Optimisation did not converge:
iteration limit reached without convergence (10)
@@ -319,7 +322,7 @@ indicates that this difference is significant as the p-value is below
<pre><code> Model df AIC BIC logLik Test L.Ratio p-value
f_parent_nlme_sfo_const 1 5 796.60 811.82 -393.30
f_parent_nlme_sfo_tc 2 6 798.60 816.86 -393.30 1 vs 2 0.00 0.998
-f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 &lt;.0001</code></pre>
+f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 &lt;.0001</code></pre>
<p>In addition to these fits, attempts were also made to include
correlations between random effects by using the log Cholesky
parameterisation of the matrix specifying them. The code used for these
@@ -341,7 +344,7 @@ effects does not improve the fits.</p>
<p>The selected model (DFOP with two-component error) fitted to the data
assuming no correlations between random effects is shown below.</p>
<div class="sourceCode" id="cb13"><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_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p>
</div>
<div class="section level4">
@@ -358,8 +361,17 @@ implemented in the saemix package, the convergence plots need to be
manually checked for every fit. We define control settings that work
well for all the parent data fits shown in this vignette.</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span>
-<span><span class="va">saemix_control</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <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">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></code></pre></div>
+<pre><code>Loading required package: npde</code></pre>
+<pre><code>Package saemix, version 3.2
+ please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre>
+<pre><code>
+Attaching package: 'saemix'</code></pre>
+<pre><code>The following objects are masked from 'package:npde':
+
+ kurtosis, skewness</code></pre>
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">saemix_control</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <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">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span>
<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="va">saemix_control_moreiter</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <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">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span>
<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
@@ -367,7 +379,7 @@ well for all the parent data fits shown in this vignette.</p>
<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<p>The convergence plot for the SFO model using constant variance is
shown below.</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<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_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div>
@@ -375,19 +387,19 @@ shown below.</p>
<p>Obviously the selected number of iterations is sufficient to reach
convergence. This can also be said for the SFO fit using the
two-component error model.</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p>
<p>When fitting the DFOP model with constant variance (see below),
parameter convergence is not as unambiguous.</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<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_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p>
-<div class="sourceCode" id="cb18"><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/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div>
<pre><code>Kinetic nonlinear mixed-effects model fit by SAEM
Structural model:
@@ -408,11 +420,11 @@ DMTA_0 97.99583 96.50079 99.4909
k1 0.06377 0.03432 0.0932
k2 0.00848 0.00444 0.0125
g 0.95701 0.91313 1.0009
-a.1 1.82141 1.65122 1.9916
-SD.DMTA_0 1.64787 0.45772 2.8380
+a.1 1.82141 1.60516 2.0377
+SD.DMTA_0 1.64787 0.45729 2.8384
SD.k1 0.57439 0.24731 0.9015
-SD.k2 0.03296 -2.50195 2.5679
-SD.g 1.10266 0.32369 1.8816</code></pre>
+SD.k2 0.03296 -2.50524 2.5712
+SD.g 1.10266 0.32354 1.8818</code></pre>
<p>While the other parameters converge to credible values, the variance
of k2 (<code>omega2.k2</code>) converges to a very small value. The
printout of the <code>saem.mmkin</code> model shows that the estimated
@@ -423,14 +435,14 @@ this model.</p>
also observe that the estimated variance of k2 becomes very small, while
being ill-defined, as illustrated by the excessive confidence interval
of <code>SD.k2</code>.</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<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_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div>
<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><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">f_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div>
<pre><code>Kinetic nonlinear mixed-effects model fit by SAEM
Structural model:
@@ -446,17 +458,17 @@ Likelihood computed by importance sampling
666 664 -323
Fitted parameters:
- estimate lower upper
-DMTA_0 98.27617 96.3088 100.2436
-k1 0.06437 0.0337 0.0950
-k2 0.00880 0.0063 0.0113
-g 0.95249 0.9100 0.9949
-a.1 1.06161 0.8625 1.2607
-b.1 0.02967 0.0226 0.0367
-SD.DMTA_0 2.06075 0.4187 3.7028
-SD.k1 0.59357 0.2561 0.9310
-SD.k2 0.00292 -10.2960 10.3019
-SD.g 1.05725 0.3808 1.7337</code></pre>
+ estimate lower upper
+DMTA_0 98.24165 96.29190 100.1914
+k1 0.06421 0.03352 0.0949
+k2 0.00866 0.00617 0.0111
+g 0.95340 0.91218 0.9946
+a.1 1.06463 0.86503 1.2642
+b.1 0.02964 0.02259 0.0367
+SD.DMTA_0 2.03611 0.40416 3.6681
+SD.k1 0.59534 0.25692 0.9338
+SD.k2 0.00042 -73.01372 73.0146
+SD.g 1.04234 0.37189 1.7128</code></pre>
<p>Doubling the number of iterations in the first phase of the algorithm
leads to a slightly lower likelihood, and therefore to slightly higher
AIC and BIC values. With even more iterations, the algorithm stops with
@@ -472,7 +484,7 @@ message.</p>
<p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and
the version with increased iterations can be compared using the model
comparison function of the saemix package:</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op">&lt;-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span></span>
<span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span>
<span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span>
@@ -480,7 +492,7 @@ comparison function of the saemix package:</p>
<span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span>
<span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div>
<pre><code>Likelihoods calculated by importance sampling</code></pre>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</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>
<span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></span></code></pre></div>
@@ -488,13 +500,13 @@ comparison function of the saemix package:</p>
SFO const 796.38 795.34
SFO tc 798.38 797.13
DFOP const 705.75 703.88
-DFOP tc 665.65 663.57
-DFOP tc more iterations 665.88 663.80</code></pre>
+DFOP tc 665.67 663.59
+DFOP tc more iterations 665.85 663.76</code></pre>
<p>In order to check the influence of the likelihood calculation
algorithms implemented in saemix, the likelihood from Gaussian
quadrature is added to the best fit, and the AIC values obtained from
the three methods are compared.</p>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op">&lt;-</span></span>
<span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span>
<span><span class="va">AIC_parent_saemix_methods</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>
@@ -504,7 +516,7 @@ the three methods are compared.</p>
<span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div>
<pre><code> is gq lin
-665.65 665.68 665.11 </code></pre>
+665.67 665.74 665.13 </code></pre>
<p>The AIC values based on importance sampling and Gaussian quadrature
are very similar. Using linearisation is known to be less accurate, but
still gives a similar value.</p>
@@ -518,7 +530,7 @@ iterations makes a lot of difference. When using the LAPACK version
coming with Debian Bullseye, the AIC based on Gaussian quadrature is
almost the same as the one obtained with the other methods, also when
using defaults for the fit.</p>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span>
<span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op">&lt;-</span></span>
<span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span>
@@ -529,7 +541,7 @@ using defaults for the fit.</p>
<span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div>
<pre><code> is gq lin
-669.77 669.36 670.95 </code></pre>
+670.09 669.37 671.29 </code></pre>
</div>
</div>
<div class="section level3">
@@ -538,7 +550,7 @@ using defaults for the fit.</p>
<p>The following table gives the AIC values obtained with both backend
packages using the same control parameters (800 iterations burn-in, 300
iterations second phase, 15 chains).</p>
-<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">AIC_all</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
<span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="st">"Degradation model"</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">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span>
@@ -549,7 +561,7 @@ iterations second phase, 15 chains).</p>
<span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</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_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span>
<span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
-<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="va">AIC_all</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Degradation model</th>
@@ -577,15 +589,15 @@ iterations second phase, 15 chains).</p>
<td align="left">DFOP</td>
<td align="left">const</td>
<td align="right">NA</td>
-<td align="right">709.26</td>
+<td align="right">704.95</td>
<td align="right">705.75</td>
</tr>
<tr class="even">
<td align="left">DFOP</td>
<td align="left">tc</td>
<td align="right">671.91</td>
-<td align="right">665.11</td>
-<td align="right">665.65</td>
+<td align="right">665.13</td>
+<td align="right">665.67</td>
</tr>
</tbody>
</table>
@@ -612,48 +624,48 @@ satisfactory precision.</p>
<div class="section level2">
<h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
</h2>
-<div class="sourceCode" id="cb32"><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/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code>R version 4.3.0 Patched (2023-05-18 r84448)
+<pre><code>R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux 12 (bookworm)
+Running under: Ubuntu 22.04.3 LTS
Matrix products: default
-BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0
+BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
- [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
- [3] LC_TIME=C LC_COLLATE=de_DE.UTF-8
- [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
- [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
+ [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
+ [3] LC_TIME=C LC_COLLATE=en_US.UTF-8
+ [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
+ [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
-[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
-time zone: Europe/Berlin
+time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
-[1] nlme_3.1-162 mkin_1.2.4 knitr_1.42
+[1] saemix_3.2 npde_3.3 nlme_3.1-163 mkin_1.2.6 knitr_1.44
loaded via a namespace (and not attached):
- [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 saemix_3.2
- [5] stringi_1.7.12 lattice_0.21-8 digest_0.6.31 magrittr_2.0.3
- [9] evaluate_0.21 grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3
-[13] jsonlite_1.8.4 DBI_1.1.3 mclust_6.0.0 gridExtra_2.3
-[17] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 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_4.3.0 parallel_4.3.0
-[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2
-[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3
-[37] stringr_1.5.0 fs_1.6.2 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 xfun_0.39
-[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 npde_3.3
-[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre>
+ [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
+ [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22
+ [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7
+[13] mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4
+[17] scales_1.2.1 codetools_0.2-19 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_4.3.1 parallel_4.3.1 memoise_2.0.1
+[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.3
+[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0
+[37] fs_1.6.3 MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3
+[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0
+[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.40
+[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0
+[53] htmltools_0.5.6.1 rmarkdown_2.23 compiler_4.3.1 </code></pre>
</div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html
index b9224bb0..dff087e4 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -134,7 +137,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 20 April 2023
-(rebuilt 2023-05-19)</h4>
+(rebuilt 2023-10-30)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small>
<div class="hidden name"><code>multistart.rmd</code></div>
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index f41dc889..8be6ba61 100644
--- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
+++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
Binary files differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index 9e206791..bc518c0c 100644
--- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
Binary files differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index c8e918cd..9ecdf4c9 100644
--- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
Binary files differ
diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html
index a9637876..095a37e2 100644
--- a/docs/articles/web_only/saem_benchmarks.html
+++ b/docs/articles/web_only/saem_benchmarks.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
</span>
</div>
@@ -74,6 +74,9 @@
<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
+ <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
+ </li>
+ <li>
<a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
@@ -134,7 +137,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-05-19)</h4>
+(rebuilt 2023-10-30)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
<div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -190,7 +193,7 @@ explanation of the following preprocessing.</p>
<div class="sourceCode" id="cb4"><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>
<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span>
-<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_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>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">kable</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>
@@ -330,7 +333,17 @@ systems. All trademarks belong to their respective owners.</p>
<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a>
</h3>
<p>Constant variance for SFO, DFOP, SFORB and HS.</p>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="48%">
+<col width="7%">
+<col width="7%">
+<col width="8%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+</colgroup>
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
@@ -412,10 +425,30 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">1.987</td>
<td align="right">2.055</td>
</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">2.998</td>
+<td align="right">6.523</td>
+<td align="right">6.126</td>
+<td align="right">4.721</td>
+</tr>
</tbody>
</table>
<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="48%">
+<col width="7%">
+<col width="7%">
+<col width="8%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+</colgroup>
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
@@ -497,6 +530,16 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">3.433</td>
<td align="right">3.595</td>
</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">5.070</td>
+<td align="right">8.464</td>
+<td align="right">8.525</td>
+<td align="right">7.599</td>
+</tr>
</tbody>
</table>
</div>
@@ -505,6 +548,14 @@ systems. All trademarks belong to their respective owners.</p>
</h3>
<p>Two-component error for DFOP-SFO and SFORB-SFO.</p>
<table class="table">
+<colgroup>
+<col width="54%">
+<col width="8%">
+<col width="8%">
+<col width="9%">
+<col width="9%">
+<col width="10%">
+</colgroup>
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
@@ -570,6 +621,14 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">12.160</td>
<td align="right">265.934</td>
</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">30.168</td>
+<td align="right">748.675</td>
+</tr>
</tbody>
</table>
</div>
@@ -577,7 +636,14 @@ systems. All trademarks belong to their respective owners.</p>
<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a>
</h3>
<p>Two-component error for SFORB-SFO3-plus</p>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="59%">
+<col width="8%">
+<col width="8%">
+<col width="10%">
+<col width="13%">
+</colgroup>
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
@@ -635,6 +701,13 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">3.2</td>
<td align="right">456.252</td>
</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">1235.028</td>
+</tr>
</tbody>
</table>
</div>

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