From db9ae6a0c9cecb92048fde6f06af1da183c09b5f Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 19 Nov 2020 15:41:24 +0100
Subject: Depend on parallel, doc improvements

By depending on parallel instead of importing it, functions to set up
and stop a cluster are always available when mkin is loaded.

The use of multicore processing in mmkin on Windows is now documented in
the help file, which brings mkin closer to a version 1.0 #9.
---
 docs/dev/reference/index.html | 63 ++++++++++++++++++++++++++++---------------
 1 file changed, 41 insertions(+), 22 deletions(-)

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

diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 36c10225..cb37f9a6 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -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>
@@ -373,6 +373,18 @@ 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="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>
@@ -446,15 +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>
@@ -484,7 +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>
@@ -496,9 +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>
@@ -508,12 +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>
@@ -524,12 +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>
@@ -544,12 +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>
@@ -664,6 +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>
-- 
cgit v1.2.1