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</span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li class="divider"> <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> <li> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li class="divider"> <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li class="divider"> <li class="dropdown-header">Performance</li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> <li class="divider"> <li class="dropdown-header">Miscellaneous</li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> </ul></li> <li> <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/jranke/mkin/" class="external-link"> <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 with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> </body></html>