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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-30 16:05:10 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-30 16:05:10 +0100
commit524a8bba89b95840b4e9215c403947a8bb76d7b2 (patch)
treef28717d46b0ac95bd56d4b84ee4fb770364b91ba /docs/dev/reference/plot.nlme.mmkin.html
parent78884beed74c18c99521b9ceeaa643e13cf94c06 (diff)
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- <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
- <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
- <span class='va'>x</span>,
- i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
- obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
- standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
- xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
- xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
- resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
- ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
- maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
- ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
- nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
- rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
- rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
- pch_ds <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'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
- col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
- lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
- frame <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</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>An object of class <code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
- </tr>
- <tr>
- <th>i</th>
- <td><p>A numeric index to select datasets for which to plot the nlme fit,
-in case plots get too large</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>standardized</th>
- <td><p>Should the residuals be standardized? Only takes effect if
-<code>resplot = "time"</code>.</p></td>
- </tr>
- <tr>
- <th>xlab</th>
- <td><p>Label for the x axis.</p></td>
- </tr>
- <tr>
- <th>xlim</th>
- <td><p>Plot range in x direction.</p></td>
- </tr>
- <tr>
- <th>resplot</th>
- <td><p>Should the residuals plotted against time or against
-predicted values?</p></td>
- </tr>
- <tr>
- <th>ymax</th>
- <td><p>Vector of maximum y axis values</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>ncol.legend</th>
- <td><p>Number of columns to use in the legend</p></td>
- </tr>
- <tr>
- <th>nrow.legend</th>
- <td><p>Number of rows to use in the legend</p></td>
- </tr>
- <tr>
- <th>rel.height.legend</th>
- <td><p>The relative height of the legend shown on top</p></td>
- </tr>
- <tr>
- <th>rel.height.bottom</th>
- <td><p>The relative height of the bottom plot row</p></td>
- </tr>
- <tr>
- <th>pch_ds</th>
- <td><p>Symbols to be used for plotting the data.</p></td>
- </tr>
- <tr>
- <th>col_ds</th>
- <td><p>Colors used for plotting the observed data and the
-corresponding model prediction lines for the different datasets.</p></td>
- </tr>
- <tr>
- <th>lty_ds</th>
- <td><p>Line types to be used for the model predictions.</p></td>
- </tr>
- <tr>
- <th>frame</th>
- <td><p>Should a frame be drawn around the plots?</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="author"><a class="anchor" href="#author"></a>Author</h2>
-
- <p>Johannes Ranke</p>
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
- <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
-<span class='va'>dfop_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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
- A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
-<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
-<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
-<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
-</div></pre>
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