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, 27 insertions, 21 deletions

diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html
index 5591d26f..38c52425 100644
--- a/docs/dev/reference/mkinresplot.html
+++ b/docs/dev/reference/mkinresplot.html
@@ -75,7 +75,7 @@ argument show_residuals = TRUE." />
       </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">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>
 
@@ -123,7 +123,7 @@ argument show_residuals = TRUE." />
       </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>
@@ -142,7 +142,7 @@ argument show_residuals = TRUE." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Function to plot residuals stored in an mkin object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small>
     <div class="hidden name"><code>mkinresplot.Rd</code></div>
     </div>
 
@@ -153,21 +153,21 @@ the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinf
 argument <code>show_residuals = TRUE</code>.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkinresplot</span>(
-  <span class='no'>object</span>,
-  <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
-  <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)),
-  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>,
-  <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span>),
-  <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
-  <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='no'>...</span>
-)</pre>
+    <pre class="usage"><span class='fu'>mkinresplot</span><span class='op'>(</span>
+  <span class='va'>object</span>,
+  obs_vars <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'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  ylab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span><span class='op'>)</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  legend <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
+  col_obs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -227,7 +227,7 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a
     </tr>
     <tr>
       <th>...</th>
-      <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td>
+      <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
     </tr>
     </table>
 
@@ -240,10 +240,16 @@ effect, namely to produce a plot.</p>
     <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted
 lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a></code> for a function
 combining the plot of the fit and the residual plot.</p></div>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='no'>model</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='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0165</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='va'>model</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>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <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><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'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='st'>"m1"</span><span class='op'>)</span>
+</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -260,7 +266,7 @@ combining the plot of the fit and the residual plot.</p></div>
 </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>
 
       </footer>