From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 3 Feb 2021 16:41:31 +0100
Subject: Prepare for v1.0.0

- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest
---
 docs/reference/index.html | 97 ++++++++++++++++++++++++++++++++++-------------
 1 file changed, 70 insertions(+), 27 deletions(-)

(limited to 'docs/reference/index.html')

diff --git a/docs/reference/index.html b/docs/reference/index.html
index e0d34e8f..c9f66992 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -163,7 +163,7 @@
       <tr>
         
         <td>
-          <p><code><a href="mkinmod.html">mkinmod()</a></code> </p>
+          <p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i>&lt;mkinmod&gt;</i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> </p>
         </td>
         <td><p>Function to set up a kinetic model with one or more state variables</p></td>
       </tr><tr>
@@ -297,12 +297,18 @@ 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="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Print method for mmkin objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
         <th colspan="2">
           <h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2>
-          <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p>
+          <p class="section-desc"><p>Create and work with nonlinear mixed effects models</p></p>
         </th>
       </tr>
       
@@ -319,9 +325,15 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="plot.nlme.mmkin.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+          <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="summary.nlme.mmkin.html">summary(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i>&lt;summary.nlme.mmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+        <td><p>Summary method for class "nlme.mmkin"</p></td>
       </tr><tr>
         
         <td>
@@ -334,6 +346,12 @@ of an mmkin object</p></td>
           <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
         </td>
         <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Create a mixed effects model from an mmkin row object</p></td>
       </tr>
     </tbody><tbody>
       <tr>
@@ -349,6 +367,24 @@ of an mmkin object</p></td>
       
       <tr>
         
+        <td>
+          <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
+        </td>
+        <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="D24_2014.html">D24_2014</a></code> </p>
+        </td>
+        <td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p>
+        </td>
+        <td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p>
         </td>
@@ -422,15 +458,15 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="mkinds.html">mkinds</a></code> </p>
+          <p><code><a href="mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
         </td>
         <td><p>A dataset class for mkin</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="print.mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
+          <p><code><a href="mkindsg.html">print(<i>&lt;mkindsg&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Print mkinds objects</p></td>
+        <td><p>A class for dataset groups for mkin</p></td>
       </tr>
     </tbody><tbody>
       <tr>
@@ -460,7 +496,7 @@ of an mmkin object</p></td>
     </tbody><tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
+          <h2 id="section-utility-functions" class="hasAnchor"><a href="#section-utility-functions" class="anchor"></a>Utility functions</h2>
           <p class="section-desc"></p>
         </th>
       </tr>
@@ -472,9 +508,9 @@ of an mmkin object</p></td>
       <tr>
         
         <td>
-          <p><code><a href="mkinsub.html">mkinsub()</a></code> </p>
+          <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p>
         </td>
-        <td><p>Function to set up a kinetic submodel for one state variable</p></td>
+        <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
       </tr><tr>
         
         <td>
@@ -484,12 +520,6 @@ of an mmkin object</p></td>
 kinetic models fitted with mkinfit</p></td>
       </tr><tr>
         
-        <td>
-          <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p>
-        </td>
-        <td><p>Produce predictions from a kinetic model using specific parameters</p></td>
-      </tr><tr>
-        
         <td>
           <p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p>
         </td>
@@ -500,12 +530,25 @@ kinetic models fitted with mkinfit</p></td>
           <p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p>
         </td>
         <td><p>Convert a dataframe from long to wide format</p></td>
-      </tr><tr>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      
+      
+    </tbody><tbody>
+      
+      
+      <tr>
         
         <td>
-          <p><code><a href="print.mkinmod.html">print(<i>&lt;mkinmod&gt;</i>)</a></code> </p>
+          <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p>
         </td>
-        <td><p>Print mkinmod objects</p></td>
+        <td><p>Produce predictions from a kinetic model using specific parameters</p></td>
       </tr><tr>
         
         <td>
@@ -520,12 +563,6 @@ kinetic models fitted with mkinfit</p></td>
         <td><p>Function to perform isometric log-ratio transformation</p></td>
       </tr><tr>
         
-        <td>
-          <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
-        </td>
-        <td><p>Two-component error model</p></td>
-      </tr><tr>
-        
         <td>
           <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
         </td>
@@ -640,6 +677,12 @@ kinetic models fitted with mkinfit</p></td>
           <p><code><a href="add_err.html">add_err()</a></code> </p>
         </td>
         <td><p>Add normally distributed errors to simulated kinetic degradation data</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
+        </td>
+        <td><p>Two-component error model</p></td>
       </tr>
     </tbody><tbody>
       <tr>
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