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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/HEAD/R/plot.mmkin.R" class="external-link"><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="Extract.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>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> legends <span class="op">=</span> <span class="fl">1</span>,</span>
<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span>
<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span>
<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span>
<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span>
<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span>
<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span>
<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one
column.</p></dd>
<dt>main</dt>
<dd><p>The main title placed on the outer margin of the plot.</p></dd>
<dt>legends</dt>
<dd><p>An index for the fits for which legends should be shown.</p></dd>
<dt>resplot</dt>
<dd><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></dd>
<dt>ylab</dt>
<dd><p>Label for the y axis.</p></dd>
<dt>standardized</dt>
<dd><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></dd>
<dt>show_errmin</dt>
<dd><p>Should the chi2 error level be shown on top of the plots
to the left?</p></dd>
<dt>errmin_var</dt>
<dd><p>The variable for which the FOCUS chi2 error value should
be shown.</p></dd>
<dt>errmin_digits</dt>
<dd><p>The number of significant digits for rounding the FOCUS
chi2 error percentage.</p></dd>
<dt>cex</dt>
<dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd>
<dt>rel.height.middle</dt>
<dd><p>The relative height of the middle plot, if more
than two rows of plots are shown.</p></dd>
<dt>ymax</dt>
<dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd>
<dt>...</dt>
<dd><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></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>The function is called for its side effect.</p>
</div>
<div id="details">
<h2>Details</h2>
<p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then
latex is being used for the formatting of the chi2 error level.</p>
</div>
<div id="author">
<h2>Author</h2>
<p>Johannes Ranke</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span>
<span class="r-in"><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" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">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></span></span>
<span class="r-in"><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></span></span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span>
<span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span>
<span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span>
<span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span>
<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span>
<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span>
<span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># Show the error models</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span>
<span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span>
<span class="r-in"><span> <span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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