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evaluation of FOCUS Example Dataset Z</a> + </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/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> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa 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='http://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><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> + + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, + <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), + <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, + <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), + <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, + <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, + <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span> +) + +<span class='fu'>plot_sep</span>( + <span class='no'>fit</span>, + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, <span class='st'>"standardized"</span>), + <span class='no'>...</span> +) + +<span class='fu'>plot_res</span>( + <span class='no'>fit</span>, + <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, + <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>FALSE</span>, <span class='fl'>TRUE</span>), + <span class='no'>...</span> +) + +<span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</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>Alias for fit introduced for compatibility with the generic S3 +method.</p></td> + </tr> + <tr> + <th>fit</th> + <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + </tr> + <tr> + <th>obs_vars</th> + <td><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></td> + </tr> + <tr> + <th>xlab</th> + <td><p>Label for the x axis.</p></td> + </tr> + <tr> + <th>ylab</th> + <td><p>Label for the y axis.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>Plot range in x direction.</p></td> + </tr> + <tr> + <th>ylim</th> + <td><p>Plot range in y direction.</p></td> + </tr> + <tr> + <th>col_obs</th> + <td><p>Colors used for plotting the observed data and the +corresponding model prediction lines.</p></td> + </tr> + <tr> + <th>pch_obs</th> + <td><p>Symbols to be used for plotting the data.</p></td> + </tr> + <tr> + <th>lty_obs</th> + <td><p>Line types to be used for the model predictions.</p></td> + </tr> + <tr> + <th>add</th> + <td><p>Should the plot be added to an existing plot?</p></td> + </tr> + <tr> + <th>legend</th> + <td><p>Should a legend be added to the plot?</p></td> + </tr> + <tr> + <th>show_residuals</th> + <td><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></td> + </tr> + <tr> + <th>show_errplot</th> + <td><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></td> + </tr> + <tr> + <th>maxabs</th> + <td><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></td> + </tr> + <tr> + <th>sep_obs</th> + <td><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></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>row_layout</th> + <td><p>Should we use a row layout where the residual plot or the +error model plot is shown to the right?</p></td> + </tr> + <tr> + <th>lpos</th> + <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as +the first argument. If not length one, this should be of the same length +as the obs_var argument.</p></td> + </tr> + <tr> + <th>inset</th> + <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td> + </tr> + <tr> + <th>show_errmin</th> + <td><p>Should the FOCUS chi2 error value be shown in the upper +margin of the plot?</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>frame</th> + <td><p>Should a frame be drawn around the plots?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td> + </tr> + <tr> + <th>standardized</th> + <td><p>When calling 'plot_res', should the residuals be +standardized in the residual plot?</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, if +<code>show_errmin = TRUE</code>.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='co'># One parent compound, one metabolite, both single first order, path from</span> +<span class='co'># parent to sink included</span> +<span class='co'># \dontrun{</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># Show the observed variables separately, with residuals</span> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> +<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># Show the observed variables separately, with the error model</span> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'># } + +</div></pre> + </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>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |