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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-30 16:05:10 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-30 16:05:10 +0100 |
| commit | 524a8bba89b95840b4e9215c403947a8bb76d7b2 (patch) | |
| tree | f28717d46b0ac95bd56d4b84ee4fb770364b91ba /docs/dev/reference/plot_mixed.html | |
| parent | 78884beed74c18c99521b9ceeaa643e13cf94c06 (diff) | |
Complete rebuild of static docs of dev version
Diffstat (limited to 'docs/dev/reference/plot_mixed.html')
| -rw-r--r-- | docs/dev/reference/plot_mixed.html | 336 |
1 files changed, 0 insertions, 336 deletions
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</ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://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 predictions from 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_mixed.R'><code>R/plot_mixed.R</code></a></small> - <div class="hidden name"><code>plot_mixed.Rd</code></div> - </div> - - <div class="ref-description"> - <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p> - </div> - - <pre class="usage"><span class='co'># S3 method for saem.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'><=</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'><=</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='va'>...</span> -<span class='op'>)</span> - -<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'><=</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'><=</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='va'>...</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 <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td> - </tr> - <tr> - <th>i</th> - <td><p>A numeric index to select datasets for which to plot the individual predictions, -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> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The functions are called for their 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'><-</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'><-</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'><-</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'><-</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_mixed-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'><-</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_mixed-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 16:07:05 2020" -#> .... -#> Minimisation finished -#> [1] "Mon Nov 9 16:07:14 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> -</div><div class='img'><img src='plot_mixed-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -</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> 1.6.1.</p> -</div> - - </footer> - </div> - - - - - </body> -</html> - - |