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<span class="fab fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <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="hidden name"><code>plot.mkinfit.Rd</code></div> - </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> - </div> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for 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 id="arguments"> - <h2>Arguments</h2> - <dl><dt>x</dt> -<dd><p>Alias for fit introduced for compatibility with the generic S3 -method.</p></dd> - - -<dt>fit</dt> -<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> - - -<dt>obs_vars</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>xlab</dt> -<dd><p>Label for the x axis.</p></dd> - - -<dt>ylab</dt> -<dd><p>Label for the y axis.</p></dd> - - -<dt>xlim</dt> -<dd><p>Plot range in x direction.</p></dd> - - -<dt>ylim</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>col_obs</dt> -<dd><p>Colors used for plotting the observed data and the -corresponding model prediction lines.</p></dd> - - -<dt>pch_obs</dt> -<dd><p>Symbols to be used for plotting the data.</p></dd> - - -<dt>lty_obs</dt> -<dd><p>Line types to be used for the model predictions.</p></dd> - - -<dt>add</dt> -<dd><p>Should the plot be added to an existing plot?</p></dd> - - -<dt>legend</dt> -<dd><p>Should a legend be added to the plot?</p></dd> - - -<dt>show_residuals</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>show_errplot</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>maxabs</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>sep_obs</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>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>row_layout</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>lpos</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>inset</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>show_errmin</dt> -<dd><p>Should the FOCUS chi2 error value be shown in the upper -margin of the plot?</p></dd> - - -<dt>errmin_digits</dt> -<dd><p>The number of significant digits for rounding the FOCUS -chi2 error percentage.</p></dd> - - -<dt>frame</dt> -<dd><p>Should a frame be drawn around the plots?</p></dd> - - -<dt>...</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>standardized</dt> -<dd><p>When calling 'plot_res', should the residuals be -standardized in the residual plot?</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, if -<code>show_errmin = TRUE</code>.</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"># 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"><-</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">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</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">#></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"><-</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">#></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> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p><p>Site built 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