diff options
author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 14:23:16 +0100 |
---|---|---|
committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 14:23:16 +0100 |
commit | 6464d3999338d34c081f360694dbc0bc0abf68cb (patch) | |
tree | 750c7196b3b7e3f995f72e62c77a3978ddca5994 /docs/dev/reference | |
parent | a52d76a13f36c112e27383af1cac3f98b1bbed0a (diff) |
Add plot method for saem.mmkin objects
Diffstat (limited to 'docs/dev/reference')
-rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 1011 -> 27839 bytes | |||
-rw-r--r-- | docs/dev/reference/Rplot002.png | bin | 57363 -> 56909 bytes | |||
-rw-r--r-- | docs/dev/reference/index.html | 6 | ||||
-rw-r--r-- | docs/dev/reference/plot.nlme.mmkin.html | 10 | ||||
-rw-r--r-- | docs/dev/reference/plot.saem.mmkin-1.png | bin | 0 -> 86076 bytes | |||
-rw-r--r-- | docs/dev/reference/plot.saem.mmkin-2.png | bin | 0 -> 164014 bytes | |||
-rw-r--r-- | docs/dev/reference/plot.saem.mmkin.html | 308 |
7 files changed, 316 insertions, 8 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 17a35806..cfc5bc2b 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 8ada7133..cd2014eb 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 825c4d27..f5621402 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -349,6 +349,12 @@ of an mmkin object</p></td> </tr><tr> <td> + <p><code><a href="plot.saem.mmkin.html">plot(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p></td> + </tr><tr> + + <td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html index 267bef05..8f5f85f7 100644 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ b/docs/dev/reference/plot.nlme.mmkin.html @@ -150,7 +150,7 @@ <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'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>, + i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</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>, @@ -165,8 +165,7 @@ 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> + 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> @@ -247,11 +246,6 @@ corresponding model prediction lines for the different datasets.</p></td> <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='plot.mkinfit.html'>plot.mkinfit</a></code> and -<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td> - </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> diff --git a/docs/dev/reference/plot.saem.mmkin-1.png b/docs/dev/reference/plot.saem.mmkin-1.png Binary files differnew file mode 100644 index 00000000..5cb33214 --- /dev/null +++ b/docs/dev/reference/plot.saem.mmkin-1.png diff --git a/docs/dev/reference/plot.saem.mmkin-2.png b/docs/dev/reference/plot.saem.mmkin-2.png Binary files differnew file mode 100644 index 00000000..67058e6c --- /dev/null +++ b/docs/dev/reference/plot.saem.mmkin-2.png diff --git a/docs/dev/reference/plot.saem.mmkin.html b/docs/dev/reference/plot.saem.mmkin.html new file mode 100644 index 00000000..d0790a98 --- /dev/null +++ b/docs/dev/reference/plot.saem.mmkin.html @@ -0,0 +1,308 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object — plot.saem.mmkin • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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</div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot an saem 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.saem.mmkin.R'><code>R/plot.saem.mmkin.R</code></a></small> + <div class="hidden name"><code>plot.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Plot an saem 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></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='saem.html'>saem.mmkin</a></code></p></td> + </tr> + <tr> + <th>i</th> + <td><p>A numeric index to select datasets for which to plot the saem 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> + <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 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'><-</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.saem.mmkin-1.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 14:21:22 2020" +#> .... +#> Minimisation finished +#> [1] "Mon Nov 9 14:21:31 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.saem.mmkin-2.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> + + |