From af7c6de4db9981ac814362c441fbac22c8faa2d7 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 24 Nov 2022 09:02:26 +0100
Subject: Start online docs of the development version

---
 docs/dev/articles/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'docs/dev/articles/index.html')

diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 395b5f7c..e04302ef 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -17,7 +17,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
-- 
cgit v1.2.1


From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 9 Jan 2023 06:22:04 +0100
Subject: Prebuilt PDF vignettes, summary_listing

---
 docs/dev/articles/index.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'docs/dev/articles/index.html')

diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index e04302ef..cd0e315f 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -90,7 +90,9 @@
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
 
-      <dl><dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
+      <dl><dt><a href="2022_wp_1.1_dmta_parent.html">Work package 1.1: Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></dt>
+        <dd>
+        </dd><dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
         <dd>
         </dd><dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt>
         <dd>
@@ -122,7 +124,7 @@
 </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>
 
       </footer></div>
-- 
cgit v1.2.1


From 9aa186eaf43d3c86a99fd08c310cefbc5dfe0612 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 28 Jan 2023 17:40:31 +0100
Subject: Build online HTML versions of prebuilt vignettes

Also, give some structure to the menu for selecting articles
---
 docs/dev/articles/index.html | 41 +++++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

(limited to 'docs/dev/articles/index.html')

diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index cd0e315f..b9571a60 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -23,7 +23,7 @@
 
     <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">
@@ -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>
@@ -90,14 +107,18 @@
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
 
-      <dl><dt><a href="2022_wp_1.1_dmta_parent.html">Work package 1.1: Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></dt>
-        <dd>
-        </dd><dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
+      <dl><dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
         <dd>
         </dd><dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt>
         <dd>
         </dd><dt><a href="mkin.html">Introduction to mkin</a></dt>
         <dd>
+        </dd><dt><a href="prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></dt>
+        <dd>
+        </dd><dt><a href="prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></dt>
+        <dd>
+        </dd><dt><a href="prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></dt>
+        <dd>
         </dd><dt><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></dt>
         <dd>
         </dd><dt><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></dt>
-- 
cgit v1.2.1