Complete rebuild of static docs

1 files changed, 30 insertions, 13 deletions

diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html
index e2a42873..fd8325c0 100644
--- a/docs/dev/reference/create_deg_func.html
+++ b/docs/dev/reference/create_deg_func.html
@@ -17,13 +17,13 @@
       </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">1.2.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development 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">
@@ -34,6 +34,8 @@
   <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>
@@ -41,22 +43,29 @@
       <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>
@@ -64,6 +73,14 @@
     <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>
@@ -131,8 +148,8 @@
 <span class="r-in"><span>    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.458    1.000     0.458        0          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.713    1.557     0.713        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.235    1.000     0.235        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.294    1.251     0.294        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
@@ -145,8 +162,8 @@
 <span class="r-in"><span>    deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.884    1.000     0.883    0.000          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.526    1.726     1.522    0.004          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.374    1.000     0.374        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.527    1.409     0.526        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
@@ -165,7 +182,7 @@
 </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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