Complete rebuild of static docs

1 files changed, 30 insertions, 13 deletions

diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index b8b36d56..81c45ab9 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -20,13 +20,13 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo
       </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">
@@ -37,6 +37,8 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo
   <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>
@@ -44,22 +46,29 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo
       <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>
@@ -67,6 +76,14 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo
     <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>
@@ -173,12 +190,12 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Level: ds</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Structure: Diagonal</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>            parent_0 log_k_parent_sink Residual</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> StdDev: 0.000368491         0.7058039 3.065183</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>             parent_0 log_k_parent_sink Residual</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> StdDev: 0.0004253489         0.7058039 3.065183</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fixed effects:  parent_0 + log_k_parent_sink ~ 1 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                       Value Std.Error DF   t-value p-value</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0          101.18323 0.7900461 43 128.07257       0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0          101.18323 0.7900461 43 128.07256       0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent_sink  -3.08708 0.4171755 43  -7.39995       0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Correlation: </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                   prnt_0</span>
@@ -186,7 +203,7 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Standardized Within-Group Residuals:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         Min          Q1         Med          Q3         Max </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> -2.38427070 -0.52059848  0.03593021  0.39987268  2.73188969 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> -2.38427071 -0.52059848  0.03593021  0.39987268  2.73188969 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Number of Observations: 47</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Number of Groups: 3 </span>
@@ -213,7 +230,7 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m
 </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>
 
       </footer></div>