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authorJohannes Ranke <johannes.ranke@jrwb.de>2025-05-12 22:16:10 +0200
committerJohannes Ranke <johannes.ranke@jrwb.de>2025-05-12 22:16:10 +0200
commitc58ccd73951b2000a7a254fb36bbd9f0733db6cd (patch)
tree82355963701c8efe4d85fd0202b08afcb440f8db /docs/articles/web_only
parenta789ea2ae74ae371476f0e1f035226d07a429a0b (diff)
Check and test locallyHEADmain
Diffstat (limited to 'docs/articles/web_only')
-rw-r--r--docs/articles/web_only/FOCUS_Z.html4
-rw-r--r--docs/articles/web_only/NAFTA_examples.html36
-rw-r--r--docs/articles/web_only/benchmarks.html62
-rw-r--r--docs/articles/web_only/compiled_models.html20
-rw-r--r--docs/articles/web_only/dimethenamid_2018.html84
-rw-r--r--docs/articles/web_only/multistart.html4
-rw-r--r--docs/articles/web_only/saem_benchmarks.html100
7 files changed, 214 insertions, 96 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index e91942ce..26268f75 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 16 January 2018
-(rebuilt 2025-02-13)</h4>
+(rebuilt 2025-05-12)</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="d-none name"><code>FOCUS_Z.rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 88551103..53e1db48 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">26 February 2019 (rebuilt
-2025-02-13)</h4>
+2025-05-12)</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="d-none name"><code>NAFTA_examples.rmd</code></div>
@@ -119,7 +119,7 @@ same.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<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">p5a</span><span class="op">)</span></span></code></pre></div>
+<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">p5a</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></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/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div>
@@ -170,7 +170,7 @@ same.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<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">p5b</span><span class="op">)</span></span></code></pre></div>
+<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">p5b</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p>
<div class="sourceCode" id="cb11"><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">p5b</span><span class="op">)</span></span></code></pre></div>
@@ -221,7 +221,7 @@ same.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
-<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">p6</span><span class="op">)</span></span></code></pre></div>
+<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">p6</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p>
<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/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div>
@@ -272,7 +272,7 @@ same.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
-<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">p7</span><span class="op">)</span></span></code></pre></div>
+<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">p7</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p>
<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">p7</span><span class="op">)</span></span></code></pre></div>
@@ -331,7 +331,7 @@ lower value for the rate constant is used here.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
-<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">p8</span><span class="op">)</span></span></code></pre></div>
+<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">p8</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p>
<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/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div>
@@ -386,7 +386,7 @@ lower value for the rate constant is used here.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
-<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">p9a</span><span class="op">)</span></span></code></pre></div>
+<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">p9a</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p>
<div class="sourceCode" id="cb35"><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">p9a</span><span class="op">)</span></span></code></pre></div>
@@ -440,7 +440,7 @@ suggest a simple exponential decline.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
-<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">p9b</span><span class="op">)</span></span></code></pre></div>
+<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">p9b</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
<div class="sourceCode" id="cb41"><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">p9b</span><span class="op">)</span></span></code></pre></div>
@@ -498,7 +498,7 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
-<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">p10</span><span class="op">)</span></span></code></pre></div>
+<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">p10</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
<div class="sourceCode" id="cb48"><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">p10</span><span class="op">)</span></span></code></pre></div>
@@ -558,7 +558,7 @@ difference in IORE model parameters between PestDF and mkin.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
-<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">p11</span><span class="op">)</span></span></code></pre></div>
+<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">p11</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
<div class="sourceCode" id="cb54"><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">p11</span><span class="op">)</span></span></code></pre></div>
@@ -624,7 +624,7 @@ overparameterisation.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r">
-<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">p12a</span><span class="op">)</span></span></code></pre></div>
+<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">p12a</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
<div class="sourceCode" id="cb62"><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">p12a</span><span class="op">)</span></span></code></pre></div>
@@ -681,7 +681,7 @@ overparameterisation.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r">
-<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">p12b</span><span class="op">)</span></span></code></pre></div>
+<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">p12b</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
<div class="sourceCode" id="cb73"><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">p12b</span><span class="op">)</span></span></code></pre></div>
@@ -732,7 +732,7 @@ overparameterisation.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb78"><pre class="downlit sourceCode r">
-<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">p13</span><span class="op">)</span></span></code></pre></div>
+<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">p13</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
<div class="sourceCode" id="cb79"><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">p13</span><span class="op">)</span></span></code></pre></div>
@@ -787,7 +787,7 @@ overparameterisation.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r">
-<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">p14</span><span class="op">)</span></span></code></pre></div>
+<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">p14</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
<div class="sourceCode" id="cb87"><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">p14</span><span class="op">)</span></span></code></pre></div>
@@ -844,7 +844,7 @@ same results in mkin and PestDF.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb94"><pre class="downlit sourceCode r">
-<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">p15a</span><span class="op">)</span></span></code></pre></div>
+<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">p15a</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
<div class="sourceCode" id="cb95"><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">p15a</span><span class="op">)</span></span></code></pre></div>
@@ -893,7 +893,7 @@ same results in mkin and PestDF.</p>
<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
-<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">p15b</span><span class="op">)</span></span></code></pre></div>
+<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">p15b</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
<div class="sourceCode" id="cb102"><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">p15b</span><span class="op">)</span></span></code></pre></div>
@@ -950,7 +950,7 @@ mkin and PestDF.</p>
<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre>
<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre>
<div class="sourceCode" id="cb109"><pre class="downlit sourceCode r">
-<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">p16</span><span class="op">)</span></span></code></pre></div>
+<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">p16</span><span class="op">)</span></span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
<div class="sourceCode" id="cb110"><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">p16</span><span class="op">)</span></span></code></pre></div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 3566be42..52e657cb 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2025-02-13)</h4>
+(rebuilt 2025-05-12)</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="d-none name"><code>benchmarks.rmd</code></div>
@@ -422,6 +422,22 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
<td align="right">1.323</td>
<td align="right">1.925</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.4.2</td>
+<td align="left">1.2.10</td>
+<td align="right">1.407</td>
+<td align="right">1.990</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.5.0</td>
+<td align="left">1.2.10</td>
+<td align="right">1.370</td>
+<td align="right">1.996</td>
+</tr>
</tbody>
</table>
</div>
@@ -703,6 +719,24 @@ for each test.</p>
<td align="right">2.153</td>
<td align="right">1.139</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.4.2</td>
+<td align="left">1.2.10</td>
+<td align="right">0.775</td>
+<td align="right">2.199</td>
+<td align="right">1.161</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.5.0</td>
+<td align="left">1.2.10</td>
+<td align="right">0.770</td>
+<td align="right">2.184</td>
+<td align="right">1.148</td>
+</tr>
</tbody>
</table>
</div>
@@ -1074,6 +1108,30 @@ dataset, i.e. one fit for each test.</p>
<td align="right">0.735</td>
<td align="right">0.981</td>
</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.4.2</td>
+<td align="left">1.2.10</td>
+<td align="right">0.433</td>
+<td align="right">0.541</td>
+<td align="right">0.576</td>
+<td align="right">1.307</td>
+<td align="right">0.744</td>
+<td align="right">0.988</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.5.0</td>
+<td align="left">1.2.10</td>
+<td align="right">0.421</td>
+<td align="right">0.536</td>
+<td align="right">0.574</td>
+<td align="right">1.315</td>
+<td align="right">0.739</td>
+<td align="right">0.997</td>
+</tr>
</tbody>
</table>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index bbf6e897..5790a964 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -83,7 +83,7 @@
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
- <h4 data-toc-skip class="date">2025-02-13</h4>
+ <h4 data-toc-skip class="date">2025-05-12</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="d-none name"><code>compiled_models.rmd</code></div>
@@ -161,10 +161,10 @@ 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 0.105</span></span>
-<span><span class="co">## 3 deSolve, compiled 1 1.333 0.140</span></span>
-<span><span class="co">## 2 Eigenvalue based 1 1.667 0.175</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 22.486 2.361</span></span></code></pre>
+<span><span class="co">## 4 analytical 1 1.000 0.111</span></span>
+<span><span class="co">## 3 deSolve, compiled 1 1.270 0.141</span></span>
+<span><span class="co">## 2 Eigenvalue based 1 1.658 0.184</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 21.973 2.439</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>
@@ -195,12 +195,12 @@ 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 0.175</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 23.937 4.189</span></span></code></pre>
+<span><span class="co">## 2 deSolve, compiled 1 1.000 0.182</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 23.808 4.333</span></span></code></pre>
<p>Here we get a performance benefit of a factor of 24 using the version
of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 1.2.9 on</p>
-<pre><code><span><span class="co">## R version 4.4.2 (2024-10-31)</span></span>
+<p>This vignette was built with mkin 1.2.10 on</p>
+<pre><code><span><span class="co">## R version 4.5.0 (2025-04-11)</span></span>
<span><span class="co">## Platform: x86_64-pc-linux-gnu</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>
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index 5d39704d..bb2509ad 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 1 July 2022,
-built on 13 Feb 2025</h4>
+built on 12 May 2025</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="d-none name"><code>dimethenamid_2018.rmd</code></div>
@@ -170,12 +170,12 @@ 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/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>
+<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>
<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/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>
+<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>
<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
@@ -187,7 +187,7 @@ 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/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>
+<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>
<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
@@ -199,7 +199,7 @@ 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/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>
+<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>
<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
@@ -289,7 +289,7 @@ 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/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>
+<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>
<p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p>
</div>
<div class="section level4">
@@ -306,17 +306,8 @@ 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></code></pre></div>
-<pre><code>Loading required package: npde</code></pre>
-<pre><code>Package saemix, version 3.3, March 2024
- 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>
+<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>
<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>
@@ -324,7 +315,7 @@ Attaching package: 'saemix'</code></pre>
<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="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><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">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div>
@@ -332,19 +323,19 @@ shown below.</p>
<p>Obviously the selected number of iterations is sufficient to reach
convergence. This can also be said for the SFO fit using the
two-component error model.</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op">&lt;-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</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="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><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="cb23"><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/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:
@@ -380,14 +371,14 @@ 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="cb25"><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_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="cb26"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/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:
@@ -429,7 +420,7 @@ 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="cb28"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><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>
@@ -437,7 +428,7 @@ 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="cb30"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><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>
@@ -451,7 +442,7 @@ DFOP tc more iterations 665.85 663.76</code></pre>
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="cb32"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><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>
@@ -475,7 +466,7 @@ 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="cb34"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><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>
@@ -495,7 +486,7 @@ 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="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><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>
@@ -506,7 +497,7 @@ 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">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div>
+<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>
<table class="table">
<thead><tr class="header">
<th align="left">Degradation model</th>
@@ -569,15 +560,15 @@ 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="cb37"><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="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 4.4.2 (2024-10-31)
+<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
@@ -594,22 +585,21 @@ attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
-[1] saemix_3.3 npde_3.5 nlme_3.1-166 mkin_1.2.9 knitr_1.49
+[1] saemix_3.3 npde_3.5 nlme_3.1-168 mkin_1.2.10 knitr_1.49
loaded via a namespace (and not attached):
- [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2
- [5] tidyselect_1.2.1 parallel_4.4.2 gridExtra_2.3 jquerylib_0.1.4
- [9] systemfonts_1.1.0 scales_1.3.0 textshaping_0.4.1 yaml_2.3.10
-[13] fastmap_1.2.0 lattice_0.22-6 ggplot2_3.5.1 R6_2.5.1
-[17] generics_0.1.3 lmtest_0.9-40 MASS_7.3-61 htmlwidgets_1.6.4
-[21] tibble_3.2.1 desc_1.4.3 munsell_0.5.1 bslib_0.8.0
-[25] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0
-[29] xfun_0.49 fs_1.6.5 sass_0.4.9 cli_3.6.3
-[33] pkgdown_2.1.1 magrittr_2.0.3 digest_0.6.37 grid_4.4.2
-[37] mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1
-[41] glue_1.8.0 codetools_0.2-20 ragg_1.3.3 zoo_1.8-12
-[45] fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 pkgconfig_2.0.3
-[49] tools_4.4.2 htmltools_0.5.8.1</code></pre>
+ [1] gtable_0.3.6 jsonlite_1.9.0 dplyr_1.1.4 compiler_4.5.0
+ [5] tidyselect_1.2.1 parallel_4.5.0 gridExtra_2.3 jquerylib_0.1.4
+ [9] systemfonts_1.2.1 scales_1.3.0 textshaping_1.0.0 yaml_2.3.10
+[13] fastmap_1.2.0 lattice_0.22-6 ggplot2_3.5.1 R6_2.6.1
+[17] generics_0.1.3 lmtest_0.9-40 MASS_7.3-65 htmlwidgets_1.6.4
+[21] tibble_3.2.1 desc_1.4.3 munsell_0.5.1 bslib_0.9.0
+[25] pillar_1.10.1 rlang_1.1.5 cachem_1.1.0 xfun_0.51
+[29] fs_1.6.5 sass_0.4.9 cli_3.6.4 pkgdown_2.1.1
+[33] magrittr_2.0.3 digest_0.6.37 grid_4.5.0 mclust_6.1.1
+[37] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.3 glue_1.8.0
+[41] codetools_0.2-20 ragg_1.3.3 zoo_1.8-13 colorspace_2.1-1
+[45] rmarkdown_2.29 tools_4.5.0 pkgconfig_2.0.3 htmltools_0.5.8.1</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 f6ab46de..a2e452bc 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 20 April 2023
-(rebuilt 2025-02-13)</h4>
+(rebuilt 2025-05-12)</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="d-none name"><code>multistart.rmd</code></div>
diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html
index 3116d0e6..1a49f6cd 100644
--- a/docs/articles/web_only/saem_benchmarks.html
+++ b/docs/articles/web_only/saem_benchmarks.html
@@ -20,7 +20,7 @@
<a class="navbar-brand me-2" href="../../index.html">mkin</a>
- <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small>
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2025-02-13)</h4>
+(rebuilt 2025-05-12)</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="d-none name"><code>saem_benchmarks.rmd</code></div>
@@ -139,7 +139,7 @@ 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">kable</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"><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>
@@ -279,11 +279,11 @@ 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 style="width:100%;" class="table">
+<table class="table">
<colgroup>
<col width="48%">
<col width="7%">
-<col width="7%">
+<col width="8%">
<col width="8%">
<col width="7%">
<col width="7%">
@@ -401,14 +401,34 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">1.949</td>
<td align="right">2.411</td>
</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">1.115</td>
+<td align="right">2.263</td>
+<td align="right">1.991</td>
+<td align="right">2.193</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">1.876</td>
+<td align="right">1.922</td>
+<td align="right">2.423</td>
+<td align="right">1.849</td>
+</tr>
</tbody>
</table>
<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
-<table style="width:100%;" class="table">
+<table class="table">
<colgroup>
<col width="48%">
<col width="7%">
-<col width="7%">
+<col width="8%">
<col width="8%">
<col width="7%">
<col width="7%">
@@ -526,6 +546,26 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">3.256</td>
<td align="right">3.322</td>
</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">2.380</td>
+<td align="right">3.147</td>
+<td align="right">3.131</td>
+<td align="right">3.331</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">2.397</td>
+<td align="right">3.443</td>
+<td align="right">3.414</td>
+<td align="right">3.311</td>
+</tr>
</tbody>
</table>
</div>
@@ -533,11 +573,11 @@ systems. All trademarks belong to their respective owners.</p>
<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a>
</h3>
<p>Two-component error for DFOP-SFO and SFORB-SFO.</p>
-<table class="table">
+<table style="width:100%;" class="table">
<colgroup>
-<col width="54%">
-<col width="8%">
-<col width="8%">
+<col width="53%">
+<col width="7%">
+<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
@@ -631,6 +671,22 @@ systems. All trademarks belong to their respective owners.</p>
<td align="right">12.420</td>
<td align="right">289.338</td>
</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">11.581</td>
+<td align="right">296.184</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">12.067</td>
+<td align="right">278.742</td>
+</tr>
</tbody>
</table>
</div>
@@ -638,13 +694,13 @@ 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 style="width:100%;" class="table">
+<table class="table">
<colgroup>
-<col width="59%">
-<col width="8%">
+<col width="58%">
<col width="8%">
<col width="10%">
-<col width="13%">
+<col width="10%">
+<col width="12%">
</colgroup>
<thead><tr class="header">
<th align="left">CPU</th>
@@ -724,6 +780,20 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">3.3</td>
<td align="right">485.836</td>
</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">486.856</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">474.550</td>
+</tr>
</tbody>
</table>
</div>

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