Fix and rebuild documentation, see NEWS

I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.

Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.

1 files changed, 84 insertions, 30 deletions

diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 41340e88..c8c91bcb 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -33,14 +33,14 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -52,6 +52,9 @@
 <li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    </li>
+<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -59,22 +62,31 @@
       <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>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li class="divider">
     </li>
+<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    </li>
+<li class="dropdown-header">Performance</li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
@@ -82,6 +94,15 @@
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    </li>
+<li class="dropdown-header">Miscellaneous</li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -105,13 +126,16 @@
 
       
 
-      </header><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
-                        <h4 data-toc-skip class="author">Johannes Ranke</h4>
+      <h1 data-toc-skip>Calculation of time weighted average
+concentrations with mkin</h1>
+                        <h4 data-toc-skip class="author">Johannes
+Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-11-17)</h4>
+            <h4 data-toc-skip class="date">Last change 18 September 2019
+(rebuilt 2023-04-20)</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>
@@ -120,13 +144,25 @@
 
     
     
-<p>Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (<em>i.e.</em> only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, <em>i.e.</em> the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.</p>
-<p>Time weighted average concentrations for the SFO, FOMC and the DFOP model are calculated using the formulas given in the FOCUS kinetics guidance <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 251)</span>:</p>
+<p>Since version 0.9.45.1 of the ‘mkin’ package, a function for
+calculating time weighted average concentrations for decline kinetics
+(<em>i.e.</em> only for the compound applied in the experiment) is
+included. Strictly speaking, they are maximum moving window time
+weighted average concentrations, <em>i.e.</em> the maximum time weighted
+average concentration that can be found when moving a time window of a
+specified width over the decline curve.</p>
+<p>Time weighted average concentrations for the SFO, FOMC and the DFOP
+model are calculated using the formulas given in the FOCUS kinetics
+guidance <span class="citation">(FOCUS Work Group on Degradation
+Kinetics 2014, 251)</span>:</p>
 <p>SFO:</p>
-<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} \]</span></p>
+<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\left( 1 -
+e^{- k t} \right)}{ k t} \]</span></p>
 <p>FOMC:</p>
-<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)}
-                   \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]</span></p>
+<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 -
+\alpha)}
+                   \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha}
+- 1 \right) \]</span></p>
 <p>DFOP:</p>
 <p><span class="math display">\[c_\textrm{twa} = \frac{c_0}{t} \left(
   \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) +
@@ -134,15 +170,25 @@
 <p>HS for <span class="math inline">\(t &gt; t_b\)</span>:</p>
 <p><span class="math display">\[c_\textrm{twa} = \frac{c_0}{t} \left(
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
-  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]</span></p>
-<p>Often, the ratio between the time weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span> and the initial concentration <span class="math inline">\(c_0\)</span></p>
-<p><span class="math display">\[f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}\]</span></p>
-<p>is needed. This can be calculated from the fitted initial concentration <span class="math inline">\(c_0\)</span> and the time weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span>, or directly from the model parameters using the following formulas:</p>
+  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)}
+\right)  \right) \]</span></p>
+<p>Often, the ratio between the time weighted average concentration
+<span class="math inline">\(c_\textrm{twa}\)</span> and the initial
+concentration <span class="math inline">\(c_0\)</span></p>
+<p><span class="math display">\[f_\textrm{twa} =
+\frac{c_\textrm{twa}}{c_0}\]</span></p>
+<p>is needed. This can be calculated from the fitted initial
+concentration <span class="math inline">\(c_0\)</span> and the time
+weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span>, or directly from the
+model parameters using the following formulas:</p>
 <p>SFO:</p>
-<p><span class="math display">\[f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} \]</span></p>
+<p><span class="math display">\[f_\textrm{twa} = \frac{\left( 1 - e^{- k
+t} \right)}{k t} \]</span></p>
 <p>FOMC:</p>
-<p><span class="math display">\[f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)}
-                   \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]</span></p>
+<p><span class="math display">\[f_\textrm{twa} = \frac{\beta}{t (1 -
+\alpha)}
+                   \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha}
+- 1 \right) \]</span></p>
 <p>DFOP:</p>
 <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left(
   \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) +
@@ -150,11 +196,19 @@
 <p>HS for <span class="math inline">\(t &gt; t_b\)</span>:</p>
 <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left(
   \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
-  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) \]</span></p>
-<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p>
-<div id="refs" class="references hanging-indent">
-<div id="ref-FOCUSkinetics2014">
-<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
+  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)}
+\right)  \right) \]</span></p>
+<p>Note that a method for calculating maximum moving window time
+weighted average concentrations for a model fitted by ‘mkinfit’ or from
+parent decline model parameters is included in the
+<code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for
+metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’
+package can be used.</p>
+<div id="refs" class="references csl-bib-body hanging-indent">
+<div id="ref-FOCUSkinetics2014" class="csl-entry">
+FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for
+Estimating Persistence and Degradation Kinetics from Environmental Fate
+Studies on Pesticides in EU Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.
 </div>
 </div>
   </div>
@@ -174,7 +228,7 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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