Change dev branch used for docs, update static docs

1 files changed, 35 insertions, 26 deletions

diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index afd3692d..98f170b6 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/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">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
       </span>
     </div>
 
@@ -26,7 +26,7 @@
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -41,6 +41,9 @@
       <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>
+    </li>
+    <li>
       <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
     <li>
@@ -95,9 +98,27 @@
         <td><p>Fit one or more kinetic models with one or more state variables to one or
 more datasets</p></td>
       </tr><tr><td>
-          <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
+          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
+        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models</p></td>
+      </tr></tbody><tbody><tr><th colspan="2">
+          <h2 id="generics">Generics <a href="#generics" class="anchor" aria-hidden="true"></a></h2>
+          <p class="section-desc"></p><p>Generic functions introduced by the package</p>
+        </th>
+      </tr></tbody><tbody><tr><td>
+          <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get convergence information</p></td>
+      </tr><tr><td>
+          <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mhmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get the names of ill-defined parameters</p></td>
+      </tr><tr><td>
+          <p><code><a href="endpoints.html">endpoints()</a></code> </p>
+        </td>
+        <td><p>Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p><p>Functions working with mkinfit objects</p>
@@ -135,11 +156,6 @@ more datasets</p></td>
         </td>
         <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
       </tr><tr><td>
-          <p><code><a href="endpoints.html">endpoints()</a></code> </p>
-        </td>
-        <td><p>Function to calculate endpoints for further use from kinetic models fitted
-with mkinfit</p></td>
-      </tr><tr><td>
           <p><code><a href="aw.html">aw()</a></code> </p>
         </td>
         <td><p>Calculate Akaike weights for model averaging</p></td>
@@ -164,9 +180,13 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr><tr><td>
+          <p><code><a href="summary.mmkin.html">summary(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="summary.mmkin.html">print(<i>&lt;summary.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Summary method for class "mmkin"</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Create and work with nonlinear mixed effects models</p>
+          <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="nlme.mmkin.html">nlme(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">print(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">update(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
@@ -177,9 +197,10 @@ of an mmkin object</p></td>
         </td>
         <td><p>Fit nonlinear mixed models with SAEM</p></td>
       </tr><tr><td>
-          <p><code><a href="nlmixr.mmkin.html">nlmixr(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="nlmixr.mmkin.html">print(<i>&lt;nlmixr.mmkin&gt;</i>)</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_model()</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_data()</a></code> </p>
+          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Fit nonlinear mixed models using nlmixr</p></td>
+        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models</p></td>
       </tr><tr><td>
           <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
         </td>
@@ -189,10 +210,6 @@ of an mmkin object</p></td>
         </td>
         <td><p>Summary method for class "nlme.mmkin"</p></td>
       </tr><tr><td>
-          <p><code><a href="summary.nlmixr.mmkin.html">summary(<i>&lt;nlmixr.mmkin&gt;</i>)</a></code> <code><a href="summary.nlmixr.mmkin.html">print(<i>&lt;summary.nlmixr.mmkin&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Summary method for class "nlmixr.mmkin"</p></td>
-      </tr><tr><td>
           <p><code><a href="summary.saem.mmkin.html">summary(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i>&lt;summary.saem.mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Summary method for class "saem.mmkin"</p></td>
@@ -209,17 +226,13 @@ of an mmkin object</p></td>
         </td>
         <td><p>Create a mixed effects model from an mmkin row object</p></td>
       </tr><tr><td>
-          <p><code><a href="reexports.html">reexports</a></code> </p>
+          <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> </p>
         </td>
         <td><p>Objects exported from other packages</p></td>
       </tr><tr><td>
           <p><code><a href="intervals.saem.mmkin.html">intervals(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
-      </tr><tr><td>
-          <p><code><a href="intervals.nlmixr.mmkin.html">intervals(<i>&lt;nlmixr.mmkin&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Confidence intervals for parameters in nlmixr.mmkin objects</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p>
@@ -342,10 +355,6 @@ kinetic models fitted with mkinfit</p></td>
         </td>
         <td><p>Function to perform isometric log-ratio transformation</p></td>
       </tr><tr><td>
-          <p><code><a href="tffm0.html">tffm0()</a></code> <code><a href="tffm0.html">invtffm0()</a></code> </p>
-        </td>
-        <td><p>Transform formation fractions as in the first published mkin version</p></td>
-      </tr><tr><td>
           <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
@@ -442,7 +451,7 @@ kinetic models fitted with mkinfit</p></td>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>