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, 34 insertions, 10 deletions

diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html
index ab02cbb3..b4d6c077 100644
--- a/docs/reference/parplot.html
+++ b/docs/reference/parplot.html
@@ -19,13 +19,13 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma
       </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">1.2.1</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">
@@ -36,6 +36,8 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <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>
@@ -43,22 +45,29 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma
       <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 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 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>
@@ -66,6 +75,14 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <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>
   <a href="../news/index.html">News</a>
@@ -103,6 +120,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
 <span><span class="fu">parplot</span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span>
+<span>  llquant <span class="op">=</span> <span class="cn">NA</span>,</span>
 <span>  scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span>
 <span>  lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span>
 <span>  main <span class="op">=</span> <span class="st">""</span>,</span>
@@ -124,8 +142,14 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
 <dd><p>The minimum likelihood of objects to be shown</p></dd>
 
 
+<dt>llquant</dt>
+<dd><p>Fractional value for selecting only the fits with higher
+likelihoods. Overrides 'llmin'.</p></dd>
+
+
 <dt>scale</dt>
-<dd><p>By default, scale parameters using the best available fit.
+<dd><p>By default, scale parameters using the best
+available fit.
 If 'median', parameters are scaled using the median parameters from all fits.</p></dd>
 
 
@@ -167,7 +191,7 @@ doi: 10.1186/s12859-021-04373-4.</p>
 </div>
 
 <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
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