Static documentation rebuilt by pkgdown

1 files changed, 63 insertions, 63 deletions

diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index df01a00b..04ef75e4 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -8,11 +8,13 @@
 
 <title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title>
 
+
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+
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@@ -32,18 +34,16 @@
 
 
 
-<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
 
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
 <meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
-  from a previous successful call to mkinfit and plots
-  the observed data together with the solution of the fitted model.
-If the current plot device is a tikz device,
-  then latex is being used for the formatting of the chi2 error level,
-  if show_errmin = TRUE." />
+from a previous successful call to mkinfit and plots the
+observed data together with the solution of the fitted model." />
 <meta name="twitter:card" content="summary" />
 
 
 
+
 <!-- mathjax -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -114,7 +114,6 @@ If the current plot device is a tikz device,
   <a href="../news/index.html">News</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -136,42 +135,34 @@ If the current plot device is a tikz device,
     </div>
 
     <div class="ref-description">
-    
     <p>Solves the differential equations with the optimised and fixed parameters
-  from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
-  the observed data together with the solution of the fitted model.</p>
-<p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device,
-  then latex is being used for the formatting of the chi2 error level,
-  if <code>show_errmin = TRUE</code>.</p>
-    
+from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the
+observed data together with the solution of the fitted model.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</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'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</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='st'>"Observed"</span>,
-  <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>),
-  <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>,
-  <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>,
-  <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)),
-  <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>,
-  <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
-  <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>),
-  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</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'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</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='st'>"Observed"</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>),
+  <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>,
+  <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>,
+  <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
 <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
 <span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)
+
 <span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre>
-    
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>x</th>
-      <td><p>Alias for fit introduced for compatibility with the generic S3 method.</p></td>
+      <td><p>Alias for fit introduced for compatibility with the generic S3
+method.</p></td>
     </tr>
     <tr>
       <th>fit</th>
@@ -179,9 +170,9 @@ If the current plot device is a tikz device,
     </tr>
     <tr>
       <th>obs_vars</th>
-      <td><p>A character vector of names of the observed variables for which the
-    data and the model should be plotted. Defauls to all observed variables
-    in the model.</p></td>
+      <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</p></td>
     </tr>
     <tr>
       <th>xlab</th>
@@ -201,7 +192,8 @@ If the current plot device is a tikz device,
     </tr>
     <tr>
       <th>col_obs</th>
-      <td><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></td>
+      <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines.</p></td>
     </tr>
     <tr>
       <th>pch_obs</th>
@@ -221,41 +213,44 @@ If the current plot device is a tikz device,
     </tr>
     <tr>
       <th>show_residuals</th>
-      <td><p>Should residuals be shown? If only one plot of the fits is shown, the
-    residual plot is in the lower third of the plot. Otherwise, i.e. if
-    "sep_obs" is given, the residual plots will be located to the right of
-    the plots of the fitted curves.</p></td>
+      <td><p>Should residuals be shown? If only one plot of the
+fits is shown, the residual plot is in the lower third of the plot.
+Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+to the right of the plots of the fitted curves.</p></td>
     </tr>
     <tr>
       <th>show_errplot</th>
-      <td><p>Should squared residuals and the error model be shown? If only one plot of
-    the fits is shown, this plot is in the lower third of the plot.
-    Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
-    to the right of the plots of the fitted curves.</p></td>
+      <td><p>Should squared residuals and the error model be shown?
+If only one plot of the fits is shown, this plot is in the lower third of
+the plot.  Otherwise, i.e. if "sep_obs" is given, the residual plots will
+be located to the right of the plots of the fitted curves.</p></td>
     </tr>
     <tr>
       <th>maxabs</th>
-      <td><p>Maximum absolute value of the residuals. This is used for the scaling of
-    the y axis and defaults to "auto".</p></td>
+      <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
     </tr>
     <tr>
       <th>sep_obs</th>
-      <td><p>Should the observed variables be shown in separate subplots? If yes, residual plots
-    requested by "show_residuals" will be shown next to, not below the plot of the fits.</p></td>
+      <td><p>Should the observed variables be shown in separate subplots?
+If yes, residual plots requested by "show_residuals" will be shown next
+to, not below the plot of the fits.</p></td>
     </tr>
     <tr>
       <th>rel.height.middle</th>
-      <td><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></td>
+      <td><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></td>
     </tr>
     <tr>
       <th>row_layout</th>
-      <td><p>Should we use a row layout where the residual plot or the error model plot is shown
-    to the right?</p></td>
+      <td><p>Should we use a row layout where the residual plot or the
+error model plot is shown to the right?</p></td>
     </tr>
     <tr>
       <th>lpos</th>
-      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as the first argument.
-    If not length one, this should be of the same length as the obs_var argument.</p></td>
+      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></td>
     </tr>
     <tr>
       <th>inset</th>
@@ -263,11 +258,13 @@ If the current plot device is a tikz device,
     </tr>
     <tr>
       <th>show_errmin</th>
-      <td><p>Should the FOCUS chi2 error value be shown in the upper margin of the plot?</p></td>
+      <td><p>Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?</p></td>
     </tr>
     <tr>
       <th>errmin_digits</th>
-      <td><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></td>
+      <td><p>The number of significant digits for rounding the FOCUS
+chi2 error percentage.</p></td>
     </tr>
     <tr>
       <th>frame</th>
@@ -278,38 +275,41 @@ If the current plot device is a tikz device,
       <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td>
     </tr>
     </table>
-    
+
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>The function is called for its side effect.</p>
-    
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then
+latex is being used for the formatting of the chi2 error level, if
+<code>show_errmin = TRUE</code>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span>
+    <pre class="examples"><div class='input'>
+<span class='co'># One parent compound, one metabolite, both single first order, path from</span>
 <span class='co'># parent to sink included</span>
 <span class='co'># \dontrun{</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='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># Show the observed variables separately</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
 <span class='co'># Show the observed variables separately, with residuals</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
-     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'>
+     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
 <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
 <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))
 
 <span class='co'># Show the observed variables separately, with the error model</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
-     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'># }
+     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'># }
+
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-      
       <li><a href="#value">Value</a></li>
-      
+      <li><a href="#details">Details</a></li>
       <li><a href="#examples">Examples</a></li>
     </ul>