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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
commit7c62da1269e8910a210ba1917d4dc62d186d5606 (patch)
tree57da1e788f84fe95352ff66d22a9da56dc86f9c3 /docs/plot.mkinfit.html
parent38f9e15f0c972c1516ae737a2bca8d7789581bbd (diff)
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-
- <h1>
- Plot the observed data and the fitted model of an mkinfit object
-</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="comment"># S3 method for mkinfit</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">fit</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">x</span><span class="keyword">,</span>
- <span class="argument">obs_vars</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">mkinmod</span><span class="keyword">$</span><span class="symbol">map</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">xlab</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"Time"</span><span class="keyword">,</span> <span class="argument">ylab</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"Observed"</span><span class="keyword">,</span>
- <span class="argument">xlim</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/range'>range</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">data</span><span class="keyword">$</span><span class="symbol">time</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">ylim</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"default"</span><span class="keyword">,</span>
- <span class="argument">col_obs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1</span><span class="keyword">:</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">pch_obs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">col_obs</span><span class="keyword">,</span>
- <span class="argument">lty_obs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">add</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">legend</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="keyword">!</span><span class="symbol">add</span><span class="keyword">,</span>
- <span class="argument">show_residuals</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">maxabs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span>
- <span class="argument">sep_obs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">rel.height.middle</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">0.9</span><span class="keyword">,</span>
- <span class="argument">lpos</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"topright"</span><span class="keyword">,</span> <span class="argument">inset</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0.05</span><span class="keyword">,</span> <span class="number">0.05</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">show_errmin</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">errmin_digits</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span>
-<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_errmin</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>x</dt>
- <dd>
- Alias for fit introduced for compatibility with the generic S3 method.
- </dd>
- <dt>fit</dt>
- <dd>
- An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
- </dd>
- <dt>obs_vars</dt>
- <dd>
- 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.
- </dd>
- <dt>xlab</dt>
- <dd>
- Label for the x axis.
- </dd>
- <dt>ylab</dt>
- <dd>
- Label for the y axis.
- </dd>
- <dt>xlim</dt>
- <dd>
- Plot range in x direction.
- </dd>
- <dt>ylim</dt>
- <dd>
- Plot range in y direction.
- </dd>
- <dt>col_obs</dt>
- <dd>
- Colors used for plotting the observed data and the corresponding model prediction lines.
- </dd>
- <dt>pch_obs</dt>
- <dd>
- Symbols to be used for plotting the data.
- </dd>
- <dt>lty_obs</dt>
- <dd>
- Line types to be used for the model predictions.
- </dd>
- <dt>add</dt>
- <dd>
- Should the plot be added to an existing plot?
- </dd>
- <dt>legend</dt>
- <dd>
- Should a legend be added to the plot?
- </dd>
- <dt>show_residuals</dt>
- <dd>
- 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
- &quot;sep_obs&quot; is given, the residual plots will be located to the right of
- the plots of the fitted curves.
- </dd>
- <dt>maxabs</dt>
- <dd>
- Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to &quot;auto&quot;.
- </dd>
- <dt>sep_obs</dt>
- <dd>
- Should the observed variables be shown in separate subplots? If yes, residual plots
- requested by &quot;show_residuals&quot; will be shown next to, not below the plot of the fits.
- </dd>
- <dt>rel.height.middle</dt>
- <dd>
- The relative height of the middle plot, if more than two rows of plots are shown.
- </dd>
- <dt>lpos</dt>
- <dd>
- Position(s) of the legend(s). Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> as the first argument.
- If not length one, this should be of the same length as the obs_var argument.
- </dd>
- <dt>inset</dt>
- <dd>
- Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> if applicable.
- </dd>
- <dt>show_errmin</dt>
- <dd>
- Should the FOCUS chi2 error value be shown in the upper margin of the plot?
- </dd>
- <dt>errmin_digits</dt>
- <dd>
- The number of significant digits for rounding the FOCUS chi2 error percentage.
- </dd>
- <dt>...</dt>
- <dd>
- Further arguments passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></code>.
- </dd>
- </dl>
-
- <div class="Description">
- <h2>Description</h2>
-
- <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="Value">
- <h2>Value</h2>
-
- <p><dl>
- The function is called for its side effect.
-</dl></p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="comment"># One parent compound, one metabolite, both single first order, path from</span>
-<span class="comment"># parent to sink included, use Levenberg-Marquardt for speed</span>
-<span class="symbol">SFO_SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Parent"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Metabolite M1"</span> <span class="keyword">)</span><span class="keyword">)</span></div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'><span class="symbol">fit</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_D</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">method.modFit</span> <span class="argument">=</span> <span class="string">"Marq"</span><span class="keyword">)</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div>
-<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
-<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div>
-<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-<span class="comment"># Show the observed variables separately</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-<span class="comment"># Show the observed variables separately, with residuals</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div>
-<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-<span class="comment"># The same can be obtained with less typing, using the convenience function plot_sep</span>
-<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div></pre>
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