Merge branch 'v1.1.2'

1 files changed, 17 insertions, 21 deletions

diff --git a/docs/dev/index.html b/docs/dev/index.html
index 9490235c..7d3abbb2 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -45,7 +45,7 @@
       </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">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
       </span>
     </div>
 
@@ -55,7 +55,7 @@
   <a href="reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -71,6 +71,9 @@
       <a href="articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
+      <a href="articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
       <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
     <li>
@@ -120,7 +123,7 @@
 </h2>
 <p>You can install the latest released version from <a href="https://cran.r-project.org/package=mkin" class="external-link">CRAN</a> from within R:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="background">Background<a class="anchor" aria-label="anchor" href="#background"></a>
@@ -149,7 +152,7 @@
 <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li>
 <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li>
 <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li>
-<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li>
+<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) can be specified as <code>error_model = "obs"</code>.</li>
 </ul>
 </div>
 <div class="section level3">
@@ -161,7 +164,7 @@
 <li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution.</li>
 <li>When parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which cannot occur in a single experiment with a single defined radiolabel position.</li>
 <li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model used by other tools for biphasic metabolite curves. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.</li>
-<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).</li>
+<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> and <a href="https://pkgdown.jrwb.de/mkin/reference/saem.html">saem.mmkin</a> and methods. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils). The saem method uses the <code>saemix</code> package as a backend. Analytical solutions suitable for use with this package have been implemented for parent only models and the most important models including one metabolite (SFO-SFO and DFOP-SFO). Fitting other models with <code>saem.mmkin</code>, while it makes use of the compiled ODE models that mkin provides, has longer run times (at least six minutes on my system).</li>
 </ul>
 </div>
 <div class="section level3">
@@ -206,26 +209,18 @@
 <li>Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)</li>
 <li>Project Number 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li>
 </ul>
+<p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for the nice collaboration on using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p>
 </div>
 <div class="section level2">
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <table class="table">
-<tr>
-<td>
-Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a>
-</td>
-</tr>
-<tr>
-<td>
-Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a>
-</td>
-</tr>
-<tr>
-<td>
-Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a>
-</td>
-</tr>
+<tr><td>Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a>
+</td></tr>
+<tr><td>Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a>
+</td></tr>
+<tr><td>Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a>
+</td></tr>
 </table>
 </div>
 <div class="section level2">
@@ -273,6 +268,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic
 <h2 data-toc-skip>Dev status</h2>
 <ul class="list-unstyled">
 <li><a href="https://cran.r-project.org/package=mkin" class="external-link"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li>
+<li><a href="https://jranke.r-universe.dev/ui#package:mkin" class="external-link"><img src="https://jranke.r-universe.dev/badges/mkin" alt="mkin status badge"></a></li>
 <li><a href="https://app.travis-ci.com/github/jranke/mkin" class="external-link"><img src="https://travis-ci.com/jranke/mkin.svg?branch=main" alt="Build Status"></a></li>
 <li><a href="https://codecov.io/github/jranke/mkin" class="external-link"><img src="https://codecov.io/github/jranke/mkin/branch/main/graphs/badge.svg" alt="codecov"></a></li>
 </ul>
@@ -289,7 +285,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic
 
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-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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