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.

1 files changed, 45 insertions, 40 deletions

diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html
index d49924c7..cd098b7d 100644
--- a/docs/dev/reference/experimental_data_for_UBA.html
+++ b/docs/dev/reference/experimental_data_for_UBA.html
@@ -60,11 +60,11 @@ Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
 Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
  (Austria, 2015, p. 16).
 Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
- (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling,
  the residues given for the metabolite were added to the parent
  value, following the recommendation of the FOCUS kinetics workgroup.
 Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
- (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ (Hellas, 2013, p. 644). Values reported as zero were set to NA, with
  the exception of the day three sampling of metabolite A2, which was set
  to one half of the LOD reported to be 1% AR.
 Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
@@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -148,7 +148,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -192,24 +192,24 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 <p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
  (Austria, 2015, p. 16).</p>
 <p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
- (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling,
  the residues given for the metabolite were added to the parent
  value, following the recommendation of the FOCUS kinetics workgroup.</p>
 <p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
- (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ (Hellas, 2013, p. 644). Values reported as zero were set to NA, with
  the exception of the day three sampling of metabolite A2, which was set
  to one half of the LOD reported to be 1% AR.</p>
 <p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
  (United Kingdom, 2014, p. 81).</p>
     </div>
 
-    <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre>
+    <pre class="usage"><span class='va'>experimental_data_for_UBA_2019</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
     <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>,
-  each containing, among others, the following components</p><dl'>
+  each containing, among others, the following components</p><dl>
     <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd>
     <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
   
@@ -227,9 +227,9 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   Version 1.1, 18 December 2014
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
+<p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
   and Behaviour</p>
-<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
+<p>Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
   environment</p>
 <p>Ranke (2019) Documentation of results obtained for the error model expertise
   written for the German Umweltbundesamt.</p>
@@ -241,35 +241,40 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
 
 <span class='co'># Model definitions</span>
-<span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
-  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
-  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>
-)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>dfop_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
-  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
-  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>
-)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>sfo_sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
-  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
-  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
-  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>
-)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>dfop_sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
-  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
-  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
-  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
-  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>
-)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>d_1_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>1</span>:<span class='fl'>2</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>d_1_2</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Soil"</span>, <span class='fl'>1</span>:<span class='fl'>2</span>)
-
-
-<span class='no'>f_1_2_tc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"DFOP-SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>dfop_sfo_sfo</span>), <span class='no'>d_1_2</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
-
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_1_2_tc</span>, <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'>
-# }</div></pre>
+<span class='va'>sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
+<span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='va'>dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
+<span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='va'>sfo_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
+  A2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
+<span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='va'>dfop_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
+  parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
+  A2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+  use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>
+<span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>d_1_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_1_2</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Soil"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>)</span>
+
+
+<span class='va'>f_1_2_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo_sfo</span><span class='op'>)</span>, <span class='va'>d_1_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_1_2_tc</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span>
+</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># }</span></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -285,7 +290,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
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