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-rw-r--r--docs/reference/plot.mkinfit.html126
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>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -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>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -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>

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