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+from a previous successful call to mkinfit and plots the
+observed data together with the solution of the fitted model."><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."><meta name="robots" content="noindex"></head><body>
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+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
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+
+      <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small>
+      <div class="d-none name"><code>plot.mkinfit.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <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>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'mkinfit'</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>  fit <span class="op">=</span> <span class="va">x</span>,</span>
+<span>  obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
+<span>  xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
+<span>  ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span>
+<span>  xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span>
+<span>  ylim <span class="op">=</span> <span class="st">"default"</span>,</span>
+<span>  col_obs <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span>,</span>
+<span>  pch_obs <span class="op">=</span> <span class="va">col_obs</span>,</span>
+<span>  lty_obs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>  add <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  legend <span class="op">=</span> <span class="op">!</span><span class="va">add</span>,</span>
+<span>  show_residuals <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  show_errplot <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  sep_obs <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span>
+<span>  row_layout <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  lpos <span class="op">=</span> <span class="st">"topright"</span>,</span>
+<span>  inset <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="fl">0.05</span>, <span class="fl">0.05</span><span class="op">)</span>,</span>
+<span>  show_errmin <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span>
+<span>  frame <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">plot_sep</span><span class="op">(</span></span>
+<span>  <span class="va">fit</span>,</span>
+<span>  show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  show_residuals <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">TRUE</span>, <span class="st">"standardized"</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">plot_res</span><span class="op">(</span></span>
+<span>  <span class="va">fit</span>,</span>
+<span>  sep_obs <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  show_errmin <span class="op">=</span> <span class="va">sep_obs</span>,</span>
+<span>  standardized <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dd><p>Alias for fit introduced for compatibility with the generic S3
+method.</p></dd>
+
+
+<dt id="arg-fit">fit<a class="anchor" aria-label="anchor" href="#arg-fit"></a></dt>
+<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
+
+
+<dt id="arg-obs-vars">obs_vars<a class="anchor" aria-label="anchor" href="#arg-obs-vars"></a></dt>
+<dd><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></dd>
+
+
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dd><p>Label for the x axis.</p></dd>
+
+
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dd><p>Label for the y axis.</p></dd>
+
+
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dd><p>Plot range in x direction.</p></dd>
+
+
+<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt>
+<dd><p>Plot range in y direction. If given as a list, plot ranges
+for the different plot rows can be given for row layout.</p></dd>
+
+
+<dt id="arg-col-obs">col_obs<a class="anchor" aria-label="anchor" href="#arg-col-obs"></a></dt>
+<dd><p>Colors used for plotting the observed data and the
+corresponding model prediction lines.</p></dd>
+
+
+<dt id="arg-pch-obs">pch_obs<a class="anchor" aria-label="anchor" href="#arg-pch-obs"></a></dt>
+<dd><p>Symbols to be used for plotting the data.</p></dd>
+
+
+<dt id="arg-lty-obs">lty_obs<a class="anchor" aria-label="anchor" href="#arg-lty-obs"></a></dt>
+<dd><p>Line types to be used for the model predictions.</p></dd>
+
+
+<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt>
+<dd><p>Should the plot be added to an existing plot?</p></dd>
+
+
+<dt id="arg-legend">legend<a class="anchor" aria-label="anchor" href="#arg-legend"></a></dt>
+<dd><p>Should a legend be added to the plot?</p></dd>
+
+
+<dt id="arg-show-residuals">show_residuals<a class="anchor" aria-label="anchor" href="#arg-show-residuals"></a></dt>
+<dd><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. If this is set to
+'standardized', a plot of the residuals divided by the standard deviation
+given by the fitted error model will be shown.</p></dd>
+
+
+<dt id="arg-show-errplot">show_errplot<a class="anchor" aria-label="anchor" href="#arg-show-errplot"></a></dt>
+<dd><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></dd>
+
+
+<dt id="arg-maxabs">maxabs<a class="anchor" aria-label="anchor" href="#arg-maxabs"></a></dt>
+<dd><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></dd>
+
+
+<dt id="arg-sep-obs">sep_obs<a class="anchor" aria-label="anchor" href="#arg-sep-obs"></a></dt>
+<dd><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></dd>
+
+
+<dt id="arg-rel-height-middle">rel.height.middle<a class="anchor" aria-label="anchor" href="#arg-rel-height-middle"></a></dt>
+<dd><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></dd>
+
+
+<dt id="arg-row-layout">row_layout<a class="anchor" aria-label="anchor" href="#arg-row-layout"></a></dt>
+<dd><p>Should we use a row layout where the residual plot or the
+error model plot is shown to the right?</p></dd>
+
+
+<dt id="arg-lpos">lpos<a class="anchor" aria-label="anchor" href="#arg-lpos"></a></dt>
+<dd><p>Position(s) of the legend(s). Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></dd>
+
+
+<dt id="arg-inset">inset<a class="anchor" aria-label="anchor" href="#arg-inset"></a></dt>
+<dd><p>Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> if applicable.</p></dd>
+
+
+<dt id="arg-show-errmin">show_errmin<a class="anchor" aria-label="anchor" href="#arg-show-errmin"></a></dt>
+<dd><p>Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?</p></dd>
+
+
+<dt id="arg-errmin-digits">errmin_digits<a class="anchor" aria-label="anchor" href="#arg-errmin-digits"></a></dt>
+<dd><p>The number of significant digits for rounding the FOCUS
+chi2 error percentage.</p></dd>
+
+
+<dt id="arg-frame">frame<a class="anchor" aria-label="anchor" href="#arg-frame"></a></dt>
+<dd><p>Should a frame be drawn around the plots?</p></dd>
+
+
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd>
+
+
+<dt id="arg-standardized">standardized<a class="anchor" aria-label="anchor" href="#arg-standardized"></a></dt>
+<dd><p>When calling 'plot_res', should the residuals be
+standardized in the residual plot?</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>The function is called for its side effect.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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, if
+<code>show_errmin = TRUE</code>.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+    <p>Johannes Ranke</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order, path from</span></span></span>
+<span class="r-in"><span><span class="co"># parent to sink included</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                   m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span><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">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span><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">SFO_SFO</span>, <span class="va">FOCUS_2006_D</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">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</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">fit</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-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 observed variables separately, with residuals</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">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, lpos <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">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>     show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-5.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The same can be obtained with less typing, using the convenience function plot_sep</span></span></span>
+<span class="r-in"><span><span class="fu">plot_sep</span><span class="op">(</span><span class="va">fit</span>, lpos <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">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-6.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Show the observed variables separately, with the error model</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">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_errplot <span class="op">=</span> <span class="cn">TRUE</span>, lpos <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">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>     show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mkinfit-7.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>
+    </div>
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