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<h1>Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small>
<div class="hidden name"><code>plot.mmkin.Rd</code></div>
</div>
<div class="ref-description">
<p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the
same model fitted for at least one dataset is shown. When it is a column,
the fit of at least one model to the same dataset is shown.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='st'>"auto"</span>,
legends <span class='op'>=</span> <span class='fl'>1</span>,
resplot <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='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Residue"</span>,
standardized <span class='op'>=</span> <span class='cn'>FALSE</span>,
show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>,
errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>,
errmin_digits <span class='op'>=</span> <span class='fl'>3</span>,
cex <span class='op'>=</span> <span class='fl'>0.7</span>,
rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>,
ymax <span class='op'>=</span> <span class='st'>"auto"</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">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one
column.</p></td>
</tr>
<tr>
<th>main</th>
<td><p>The main title placed on the outer margin of the plot.</p></td>
</tr>
<tr>
<th>legends</th>
<td><p>An index for the fits for which legends should be shown.</p></td>
</tr>
<tr>
<th>resplot</th>
<td><p>Should the residuals plotted against time, using
<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
</tr>
<tr>
<th>ylab</th>
<td><p>Label for the y axis.</p></td>
</tr>
<tr>
<th>standardized</th>
<td><p>Should the residuals be standardized? This option
is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
<code>resplot = "time"</code>.</p></td>
</tr>
<tr>
<th>show_errmin</th>
<td><p>Should the chi2 error level be shown on top of the plots
to the left?</p></td>
</tr>
<tr>
<th>errmin_var</th>
<td><p>The variable for which the FOCUS chi2 error value should
be shown.</p></td>
</tr>
<tr>
<th>errmin_digits</th>
<td><p>The number of significant digits for rounding the FOCUS
chi2 error percentage.</p></td>
</tr>
<tr>
<th>cex</th>
<td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</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>
</tr>
<tr>
<th>ymax</th>
<td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinresplot.html'>mkinresplot</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.</p>
<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='co'># \dontrun{</span>
<span class='co'># Only use one core not to offend CRAN checks</span>
<span class='va'>fits</span> <span class='op'><-</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"HS"</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'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span>
cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span>
#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
<span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
<span class='co'># generated by pkgdown, as far as I know).</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span>
</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the error models</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
</div></pre>
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