Build online HTML versions of prebuilt vignettes

Also, give some structure to the menu for selecting articles

1 files changed, 29 insertions, 7 deletions

diff --git a/docs/dev/index.html b/docs/dev/index.html
index 993b8eea..64fd2651 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -52,7 +52,7 @@
     <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">
@@ -64,6 +64,9 @@
 <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>
@@ -71,22 +74,31 @@
       <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>
@@ -94,6 +106,15 @@
     <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>
@@ -214,6 +235,7 @@
 <li>Project Number 112407 (Testing the feasibility of using an error model according to Rocke and Lorenzato for more realistic parameter estimates in the kinetic evaluation of degradation data, 2018-2019)</li>
 <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>
+<li>Project Number 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data)</li>
 </ul>
 <p>Thanks to everyone involved for collaboration and support!</p>
 <p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for her interest and support for using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p>