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-rw-r--r--docs/dev/articles/FOCUS_D.html12
-rw-r--r--docs/dev/articles/FOCUS_L.html62
-rw-r--r--docs/dev/articles/index.html4
-rw-r--r--docs/dev/articles/mkin.html12
-rw-r--r--docs/dev/articles/prebuilt/2022_cyan_pathway.html263
-rw-r--r--docs/dev/articles/prebuilt/2022_dmta_parent.html140
-rw-r--r--docs/dev/articles/prebuilt/2022_dmta_pathway.html51
-rw-r--r--docs/dev/articles/twa.html4
-rw-r--r--docs/dev/articles/web_only/FOCUS_Z.html4
-rw-r--r--docs/dev/articles/web_only/NAFTA_examples.html4
-rw-r--r--docs/dev/articles/web_only/benchmarks.html82
-rw-r--r--docs/dev/articles/web_only/compiled_models.html20
-rw-r--r--docs/dev/articles/web_only/dimethenamid_2018.html43
-rw-r--r--docs/dev/articles/web_only/multistart.html4
-rw-r--r--docs/dev/articles/web_only/saem_benchmarks.html96
15 files changed, 470 insertions, 331 deletions
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index 4a9406de..ddfb268d 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ D</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change 31 January 2019
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.rmd</code></div>
@@ -238,10 +238,10 @@ the <code>mkinparplot</code> function.</p>
<code>summary</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:12 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:12 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:10 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:10 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 853194fb..9500e661 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,8 +135,8 @@ to L3</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
- <h4 data-toc-skip class="date">Last change 18 May 2022
-(rebuilt 2023-04-16)</h4>
+ <h4 data-toc-skip class="date">Last change 18 May 2023
+(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -170,10 +170,10 @@ report.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">m.L1.SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:11 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:11 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
@@ -277,10 +277,10 @@ objects.</p>
<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span>
<span><span class="co">## is doubtful</span></span></code></pre>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
@@ -428,10 +428,10 @@ kinetics.</p>
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
@@ -512,10 +512,10 @@ the data.</p>
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:15 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -629,10 +629,10 @@ using square brackets for indexing which will result in the use of the
summary and plot functions working on mkinfit objects.</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:15 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -756,10 +756,10 @@ passes is slightly lower for the FOMC model. However, the difference
appears negligible.</p>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:16 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
@@ -821,10 +821,10 @@ appears negligible.</p>
<span><span class="co">## parent 106 352</span></span></code></pre>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span>
-<span><span class="co">## R version used for fitting: 4.2.3 </span></span>
-<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span>
-<span><span class="co">## Date of summary: Sun Apr 16 08:35:16 2023 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span>
+<span><span class="co">## R version used for fitting: 4.3.0 </span></span>
+<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span>
+<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Equations:</span></span>
<span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index c9116643..e11f3f16 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -111,7 +111,7 @@
<dd>
</dd><dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt>
<dd>
- </dd><dt><a href="mkin.html">Introduction to mkin</a></dt>
+ </dd><dt><a href="mkin.html">Short introduction to mkin</a></dt>
<dd>
</dd><dt><a href="prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></dt>
<dd>
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index fa3ac11c..e0011a5a 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -5,13 +5,13 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Introduction to mkin • mkin</title>
+<title>Short introduction to mkin • mkin</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin">
+<script src="../pkgdown.js"></script><meta property="og:title" content="Short introduction to mkin">
<meta property="og:description" content="mkin">
<meta name="robots" content="noindex">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -130,12 +130,12 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
- <h1 data-toc-skip>Introduction to mkin</h1>
+ <h1 data-toc-skip>Short introduction to mkin</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
- <h4 data-toc-skip class="date">Last change 15 February 2021
-(rebuilt 2023-04-16)</h4>
+ <h4 data-toc-skip class="date">Last change 18 May 2023
+(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small>
<div class="hidden name"><code>mkin.rmd</code></div>
diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
index 7bb0fa5b..2359969e 100644
--- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ residue data on cyantraniliprole</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change on 20 April 2023,
-last compiled on 20 April 2023</h4>
+last compiled on 19 Mai 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small>
<div class="hidden name"><code>2022_cyan_pathway.rmd</code></div>
@@ -156,7 +156,7 @@ be fitted with the mkin package.</p>
173340 (Application of nonlinear hierarchical models to the kinetic
evaluation of chemical degradation data) of the German Environment
Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.4 which is currently under
+<p>The mkin package is used in version 1.2.5 which is currently under
development. The newly introduced functionality that is used here is a
simplification of excluding random effects for a set of fits based on a
related set of fits with a reduced model, and the documentation of the
@@ -2220,10 +2220,10 @@ Hierarchical SFO path 1 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:33:05 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:42:02 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - k_cyan * cyan
@@ -2236,7 +2236,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 438.011 s
+Fitted in 443.997 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -2348,10 +2348,10 @@ Hierarchical SFO path 1 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:32:55 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:42:01 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - k_cyan * cyan
@@ -2364,7 +2364,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 427.249 s
+Fitted in 442.545 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -2478,10 +2478,10 @@ Hierarchical FOMC path 1 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:33:49 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:42:38 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2496,7 +2496,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 481.497 s
+Fitted in 479.463 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -2623,10 +2623,10 @@ Hierarchical FOMC path 1 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:33:59 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:42:53 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2641,7 +2641,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 491.071 s
+Fitted in 494.121 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -2761,10 +2761,10 @@ Hierarchical DFOP path 1 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:34:33 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:43:22 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2783,7 +2783,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 525.551 s
+Fitted in 523.691 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -2907,10 +2907,10 @@ Hierarchical DFOP path 1 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:37:03 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:46:08 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2929,7 +2929,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 675.804 s
+Fitted in 689.217 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -3053,10 +3053,10 @@ Hierarchical SFORB path 1 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:34:43 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:43:37 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3074,7 +3074,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 535.818 s
+Fitted in 538.025 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -3218,10 +3218,10 @@ Hierarchical SFORB path 1 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:37:02 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:45:51 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3239,7 +3239,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 674.859 s
+Fitted in 672.309 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -3383,10 +3383,10 @@ Hierarchical HS path 1 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:34:41 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:43:26 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ifelse(time &lt;= tb, k1, k2) * cyan
@@ -3401,7 +3401,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 533.787 s
+Fitted in 526.974 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -3525,10 +3525,10 @@ Hierarchical HS path 1 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:34:39 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:43:29 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ifelse(time &lt;= tb, k1, k2) * cyan
@@ -3543,7 +3543,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 531.084 s
+Fitted in 529.515 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -3673,10 +3673,10 @@ Hierarchical FOMC path 2 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:45:51 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:54:58 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3691,7 +3691,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 517.002 s
+Fitted in 519.639 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -3837,10 +3837,10 @@ Hierarchical FOMC path 2 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:45:39 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:54:41 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3855,7 +3855,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 505.619 s
+Fitted in 503.222 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -3983,10 +3983,10 @@ Hierarchical DFOP path 2 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:46:46 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:55:53 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4006,7 +4006,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 572.382 s
+Fitted in 574.8 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -4174,10 +4174,10 @@ Hierarchical DFOP path 2 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:49:18 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:58:32 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4197,7 +4197,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 724.515 s
+Fitted in 733.398 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -4365,10 +4365,10 @@ Hierarchical SFORB path 2 fit with constant variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:46:33 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:55:51 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4386,7 +4386,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 559.097 s
+Fitted in 572.747 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -4561,10 +4561,10 @@ Hierarchical SFORB path 2 fit with two-component error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 20:49:20 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 17:58:21 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4582,7 +4582,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 726.293 s
+Fitted in 722.847 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -4762,10 +4762,10 @@ error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 21:02:39 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:12:10 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4780,7 +4780,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 796.615 s
+Fitted in 816.454 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -4905,10 +4905,10 @@ variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 21:04:15 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:13:38 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4928,7 +4928,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 893.328 s
+Fitted in 904.25 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -5071,10 +5071,10 @@ error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 21:04:33 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:00 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -5094,7 +5094,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 910.788 s
+Fitted in 926.094 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -5237,10 +5237,10 @@ variance
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 21:04:09 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:13:34 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5258,7 +5258,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 887.369 s
+Fitted in 900.859 s
Using 300, 100 iterations and 10 chains
Variance model: Constant variance
@@ -5408,10 +5408,10 @@ error
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.2.3
-Date of fit: Thu Apr 20 21:04:32 2023
-Date of summary: Thu Apr 20 21:04:34 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:13:37 2023
+Date of summary: Fri May 19 18:14:01 2023
Equations:
d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5429,7 +5429,7 @@ Data:
Model predictions using solution type deSolve
-Fitted in 910.017 s
+Fitted in 903.326 s
Using 300, 100 iterations and 10 chains
Variance model: Two-component variance function
@@ -5578,13 +5578,13 @@ JSE76 26.89 89.33 NA NA NA
<div class="section level3">
<h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
</h3>
-<pre><code>R version 4.2.3 (2023-03-15)
+<pre><code>R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
-BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
@@ -5594,37 +5594,40 @@ locale:
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
-[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4
+[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5
loaded via a namespace (and not attached):
- [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38
- [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0
- [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7
-[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7
-[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3
-[21] readxl_1.4.2 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0
-[25] gtable_0.3.3 cellranger_1.1.0 ragg_1.2.5 codetools_0.2-19
-[29] memoise_2.0.1 evaluate_0.20 inline_0.3.19 callr_3.7.3
-[33] fastmap_1.1.1 ps_1.7.4 lmtest_0.9-40 fansi_1.0.4
-[37] highr_0.10 scales_1.2.1 cachem_1.0.7 desc_1.4.2
-[41] jsonlite_1.8.4 systemfonts_1.0.4 fs_1.6.1 textshaping_0.3.6
-[45] gridExtra_2.3 ggplot2_3.4.2 digest_0.6.31 stringi_1.7.12
-[49] processx_3.8.0 dplyr_1.1.1 grid_4.2.3 rprojroot_2.0.3
-[53] cli_3.6.1 tools_4.2.3 magrittr_2.0.3 sass_0.4.5
-[57] tibble_3.2.1 crayon_1.5.2 pkgconfig_2.0.3 prettyunits_1.1.1
-[61] rmarkdown_2.21 R6_2.5.1 mclust_6.0.0 nlme_3.1-162
-[65] compiler_4.2.3 </code></pre>
+ [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
+ [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21
+ [9] grid_4.3.0 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3
+[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35
+[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3
+[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19
+[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2
+[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7
+[33] inline_0.3.19 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2
+[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1
+[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2
+[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2
+[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3
+[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39
+[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5
+[61] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1
+[65] readxl_1.4.2 </code></pre>
</div>
<div class="section level3">
<h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
</h3>
<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
-<pre><code>MemTotal: 64936316 kB</code></pre>
+<pre><code>MemTotal: 64925476 kB</code></pre>
</div>
</div>
</div>
diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html
index 92259add..45a925b3 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_parent.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ with residue data on dimethenamid and dimethenamid-P</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change on 5 January
-2023, last compiled on 16 April 2023</h4>
+2023, last compiled on 19 Mai 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small>
<div class="hidden name"><code>2022_dmta_parent.rmd</code></div>
@@ -155,7 +155,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p>
173340 (Application of nonlinear hierarchical models to the kinetic
evaluation of chemical degradation data) of the German Environment
Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.3. It contains the test data
+<p>The mkin package is used in version 1.2.5. It contains the test data
and the functions used in the evaluations. The <code>saemix</code>
package is used as a backend for fitting the NLHM, but is also loaded to
make the convergence plot function available.</p>
@@ -1287,10 +1287,10 @@ Plot of the final NLHM DFOP fit
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div>
<pre><code>saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:51 2023
-Date of summary: Sat Jan 28 11:22:52 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:27 2023
+Date of summary: Fri May 19 18:14:28 2023
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1302,7 +1302,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 3.74 s
+Fitted in 4.477 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1463,10 +1463,10 @@ Hierarchical mkin fit of the SFO model with error model const
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:44 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:19 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - k_DMTA * DMTA
@@ -1476,7 +1476,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 0.982 s
+Fitted in 1.091 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1535,10 +1535,10 @@ Hierarchical mkin fit of the SFO model with error model tc
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:46 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:21 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - k_DMTA * DMTA
@@ -1548,7 +1548,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 2.39 s
+Fitted in 2.517 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1609,10 +1609,10 @@ Hierarchical mkin fit of the FOMC model with error model const
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:45 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:20 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1622,7 +1622,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.552 s
+Fitted in 1.25 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1686,10 +1686,10 @@ Hierarchical mkin fit of the FOMC model with error model tc
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:46 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:21 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1699,7 +1699,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 2.764 s
+Fitted in 2.666 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1765,10 +1765,10 @@ Hierarchical mkin fit of the DFOP model with error model const
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:45 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:20 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1780,7 +1780,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.649 s
+Fitted in 1.639 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1849,10 +1849,10 @@ Hierarchical mkin fit of the DFOP model with error model tc
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:46 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:22 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1864,7 +1864,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 3.288 s
+Fitted in 3.435 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1935,10 +1935,10 @@ Hierarchical mkin fit of the HS model with error model const
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:45 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:20 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - ifelse(time &lt;= tb, k1, k2) * DMTA
@@ -1948,7 +1948,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 2.006 s
+Fitted in 1.946 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -2017,10 +2017,10 @@ Hierarchical mkin fit of the HS model with error model tc
</caption>
<pre><code>
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.2
-R version used for fitting: 4.2.2
-Date of fit: Sat Jan 28 11:22:46 2023
-Date of summary: Sat Jan 28 11:23:57 2023
+mkin version used for pre-fitting: 1.2.5
+R version used for fitting: 4.3.0
+Date of fit: Fri May 19 18:14:22 2023
+Date of summary: Fri May 19 18:15:34 2023
Equations:
d_DMTA/dt = - ifelse(time &lt;= tb, k1, k2) * DMTA
@@ -2030,7 +2030,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 3.267 s
+Fitted in 3.626 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -2144,13 +2144,13 @@ Convergence plot for the NLHM HS fit with two-component error
<div class="section level3">
<h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
</h3>
-<pre><code>R version 4.2.2 Patched (2022-11-10 r83330)
+<pre><code>R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux bookworm/sid
+Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
-BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
@@ -2160,35 +2160,37 @@ locale:
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
-[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.2
+[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5
loaded via a namespace (and not attached):
- [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.35
- [5] bslib_0.4.2 purrr_1.0.0 lattice_0.20-45 colorspace_2.0-3
- [9] vctrs_0.5.1 generics_0.1.3 htmltools_0.5.4 yaml_2.3.6
-[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.7 jquerylib_0.1.4
-[17] pillar_1.8.1 glue_1.6.2 DBI_1.1.3 lifecycle_1.0.3
-[21] stringr_1.5.0 munsell_0.5.0 gtable_0.3.1 ragg_1.2.4
-[25] codetools_0.2-18 memoise_2.0.1 evaluate_0.19 fastmap_1.1.0
-[29] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.1
-[33] cachem_1.0.6 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4
-[37] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.0
-[41] digest_0.6.31 stringi_1.7.8 dplyr_1.0.10 grid_4.2.2
-[45] rprojroot_2.0.3 cli_3.5.0 tools_4.2.2 magrittr_2.0.3
-[49] sass_0.4.4 tibble_3.1.8 pkgconfig_2.0.3 assertthat_0.2.1
-[53] rmarkdown_2.19 R6_2.5.1 mclust_6.0.0 nlme_3.1-161
-[57] compiler_4.2.2 </code></pre>
+ [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
+ [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21
+ [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4
+[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1
+[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6
+[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
+[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 memoise_2.0.1
+[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2
+[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0
+[37] fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2
+[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3
+[45] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39
+[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5
+[53] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 </code></pre>
</div>
<div class="section level3">
<h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
</h3>
<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
-<pre><code>MemTotal: 64940452 kB</code></pre>
+<pre><code>MemTotal: 64925476 kB</code></pre>
</div>
</div>
</div>
diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
index 959f3429..1861db06 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ residue data on dimethenamid and dimethenamid-P</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change on 20 April 2023,
-last compiled on 20 April 2023</h4>
+last compiled on 19 Mai 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small>
<div class="hidden name"><code>2022_dmta_pathway.rmd</code></div>
@@ -156,7 +156,7 @@ can be fitted with the mkin package.</p>
173340 (Application of nonlinear hierarchical models to the kinetic
evaluation of chemical degradation data) of the German Environment
Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.4, which is currently under
+<p>The mkin package is used in version 1.2.5, which is currently under
development. It contains the test data, and the functions used in the
evaluations. The <code>saemix</code> package is used as a backend for
fitting the NLHM, but is also loaded to make the convergence plot
@@ -1972,13 +1972,13 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path
<div class="section level3">
<h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
</h3>
-<pre><code>R version 4.2.3 (2023-03-15)
+<pre><code>R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
-BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
@@ -1988,36 +1988,39 @@ locale:
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
-[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4
+[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5
loaded via a namespace (and not attached):
- [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38
- [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0
- [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7
-[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7
-[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3
-[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.3
-[25] ragg_1.2.5 codetools_0.2-19 memoise_2.0.1 evaluate_0.20
-[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.1 ps_1.7.4
-[33] lmtest_0.9-40 fansi_1.0.4 highr_0.10 scales_1.2.1
-[37] cachem_1.0.7 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4
-[41] fs_1.6.1 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.2
-[45] digest_0.6.31 stringi_1.7.12 processx_3.8.0 dplyr_1.1.1
-[49] grid_4.2.3 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3
-[53] magrittr_2.0.3 sass_0.4.5 tibble_3.2.1 crayon_1.5.2
-[57] pkgconfig_2.0.3 prettyunits_1.1.1 rmarkdown_2.21 R6_2.5.1
-[61] mclust_6.0.0 nlme_3.1-162 compiler_4.2.3 </code></pre>
+ [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
+ [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21
+ [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4
+[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3
+[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1
+[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6
+[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1
+[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19
+[33] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0
+[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12
+[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 ragg_1.2.5
+[45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7
+[49] bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 glue_1.6.2
+[53] systemfonts_1.0.4 highr_0.10 xfun_0.39 tibble_3.2.1
+[57] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162
+[61] rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1</code></pre>
</div>
<div class="section level3">
<h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
</h3>
<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
-<pre><code>MemTotal: 64936316 kB</code></pre>
+<pre><code>MemTotal: 64925476 kB</code></pre>
</div>
</div>
</div>
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index 4aa8f5b1..b71f0e01 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ concentrations with mkin</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change 18 September 2019
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small>
<div class="hidden name"><code>twa.rmd</code></div>
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 979cf2c6..917a6865 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,7 +135,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 16 January 2018
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</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>
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index 9feecfce..e4e457fc 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ to the US EPA SOP for the NAFTA guidance</h1>
Ranke</h4>
<h4 data-toc-skip class="date">26 February 2019 (rebuilt
-2023-04-16)</h4>
+2023-05-19)</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/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 87bdd55f..b3c12f66 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,7 +135,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</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>
@@ -423,8 +423,24 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
-<td align="right">1.404</td>
-<td align="right">1.933</td>
+<td align="right">1.406</td>
+<td align="right">1.948</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">1.386</td>
+<td align="right">1.960</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">1.400</td>
+<td align="right">1.936</td>
</tr>
</tbody>
</table>
@@ -649,9 +665,27 @@ for each test.</p>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
-<td align="right">0.797</td>
-<td align="right">2.124</td>
-<td align="right">1.182</td>
+<td align="right">0.793</td>
+<td align="right">2.109</td>
+<td align="right">1.178</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">0.779</td>
+<td align="right">2.080</td>
+<td align="right">1.106</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">0.800</td>
+<td align="right">2.118</td>
+<td align="right">1.172</td>
</tr>
</tbody>
</table>
@@ -958,11 +992,35 @@ dataset, i.e. one fit for each test.</p>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
<td align="right">0.432</td>
-<td align="right">0.551</td>
-<td align="right">0.616</td>
-<td align="right">1.039</td>
-<td align="right">0.734</td>
-<td align="right">0.981</td>
+<td align="right">0.549</td>
+<td align="right">0.609</td>
+<td align="right">1.052</td>
+<td align="right">0.743</td>
+<td align="right">0.989</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">0.410</td>
+<td align="right">0.526</td>
+<td align="right">0.553</td>
+<td align="right">1.249</td>
+<td align="right">0.712</td>
+<td align="right">0.948</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">0.433</td>
+<td align="right">0.558</td>
+<td align="right">0.618</td>
+<td align="right">1.053</td>
+<td align="right">0.745</td>
+<td align="right">0.986</td>
</tr>
</tbody>
</table>
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index e7905860..a0b34dda 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,7 +135,7 @@ definitions in mkin</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
- <h4 data-toc-skip class="date">2023-04-16</h4>
+ <h4 data-toc-skip class="date">2023-05-19</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>
@@ -214,10 +214,10 @@ 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 1.276 0.134</span></span>
-<span><span class="co">## 2 Eigenvalue based 1 1.762 0.185</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 21.914 2.301</span></span></code></pre>
+<span><span class="co">## 4 analytical 1 1.000 0.108</span></span>
+<span><span class="co">## 3 deSolve, compiled 1 1.259 0.136</span></span>
+<span><span class="co">## 2 Eigenvalue based 1 1.704 0.184</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 21.574 2.330</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>
@@ -248,12 +248,12 @@ 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 0.176</span></span>
-<span><span class="co">## 1 deSolve, not compiled 1 23.938 4.213</span></span></code></pre>
+<span><span class="co">## 2 deSolve, compiled 1 1.000 0.178</span></span>
+<span><span class="co">## 1 deSolve, not compiled 1 23.708 4.220</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 1.2.3 on</p>
-<pre><code><span><span class="co">## R version 4.2.3 (2023-03-15)</span></span>
+<p>This vignette was built with mkin 1.2.5 on</p>
+<pre><code><span><span class="co">## R version 4.3.0 (2023-04-21)</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>
diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html
index eb4a11a5..60e65367 100644
--- a/docs/dev/articles/web_only/dimethenamid_2018.html
+++ b/docs/dev/articles/web_only/dimethenamid_2018.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -136,7 +136,7 @@ from 2018</h1>
Ranke</h4>
<h4 data-toc-skip class="date">Last change 1 July 2022,
-built on 16 Apr 2023</h4>
+built on 19 May 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>
@@ -615,13 +615,13 @@ satisfactory precision.</p>
</h2>
<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 4.2.3 (2023-03-15)
+<pre><code>R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
-BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
@@ -631,27 +631,30 @@ locale:
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
-[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.3 knitr_1.42
+[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.5 knitr_1.42
loaded via a namespace (and not attached):
- [1] highr_0.10 pillar_1.9.0 bslib_0.4.2 compiler_4.2.3
- [5] jquerylib_0.1.4 tools_4.2.3 mclust_6.0.0 digest_0.6.31
- [9] tibble_3.2.1 jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1
-[13] lifecycle_1.0.3 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3
-[17] rlang_1.1.0 DBI_1.1.3 cli_3.6.1 yaml_2.3.7
-[21] parallel_4.2.3 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1
-[25] gridExtra_2.3 dplyr_1.1.1 stringr_1.5.0 generics_0.1.3
-[29] desc_1.4.2 fs_1.6.1 vctrs_0.6.1 sass_0.4.5
-[33] systemfonts_1.0.4 tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40
-[37] grid_4.2.3 glue_1.6.2 R6_2.5.1 textshaping_0.3.6
-[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2
-[45] magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 htmltools_0.5.5
-[49] colorspace_2.1-0 ragg_1.2.5 utf8_1.2.3 stringi_1.7.12
-[53] munsell_0.5.0 cachem_1.0.7 zoo_1.8-12 </code></pre>
+ [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
+ [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21
+ [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4
+[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1
+[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6
+[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
+[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 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 highr_0.10
+[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0
+[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre>
</div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index 2de5059c..7855f177 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,7 +135,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 20 April 2023
-(rebuilt 2023-04-20)</h4>
+(rebuilt 2023-05-19)</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/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 66740a11..22acf655 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -34,7 +34,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
</span>
</div>
@@ -135,7 +135,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</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>
@@ -398,10 +398,30 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
-<td align="right">1.389</td>
-<td align="right">2.300</td>
-<td align="right">1.880</td>
-<td align="right">2.355</td>
+<td align="right">1.419</td>
+<td align="right">2.374</td>
+<td align="right">1.926</td>
+<td align="right">2.398</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">0.972</td>
+<td align="right">2.550</td>
+<td align="right">1.987</td>
+<td align="right">2.055</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">0.994</td>
+<td align="right">2.546</td>
+<td align="right">1.999</td>
+<td align="right">2.070</td>
</tr>
</tbody>
</table>
@@ -473,10 +493,30 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
-<td align="right">2.300</td>
-<td align="right">3.075</td>
-<td align="right">3.206</td>
-<td align="right">3.471</td>
+<td align="right">2.348</td>
+<td align="right">3.134</td>
+<td align="right">3.253</td>
+<td align="right">3.530</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">2.127</td>
+<td align="right">3.587</td>
+<td align="right">3.433</td>
+<td align="right">3.595</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">2.152</td>
+<td align="right">3.316</td>
+<td align="right">3.309</td>
+<td align="right">3.337</td>
</tr>
</tbody>
</table>
@@ -540,8 +580,24 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
-<td align="right">12.951</td>
-<td align="right">294.082</td>
+<td align="right">12.841</td>
+<td align="right">292.688</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">12.160</td>
+<td align="right">265.934</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">11.249</td>
+<td align="right">290.918</td>
</tr>
</tbody>
</table>
@@ -599,7 +655,21 @@ systems. All trademarks belong to their respective owners.</p>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
-<td align="right">477.297</td>
+<td align="right">483.027</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">456.252</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">479.637</td>
</tr>
</tbody>
</table>

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