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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
commitaf7c6de4db9981ac814362c441fbac22c8faa2d7 (patch)
tree33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/mkinerrplot.html
parent8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)
Start online docs of the development version
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diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html
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observed variables from an mkinfit object. In addition, one or more dashed
line(s) show the fitted error model. A combined plot of the fitted model
and this error model plot can be obtained with plot.mkinfit
-using the argument show_errplot = TRUE." />
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+using the argument show_errplot = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -76,23 +21,21 @@ using the argument show_errplot = TRUE." />
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- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
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+ <ul class="nav navbar-nav"><li>
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@@ -102,48 +45,50 @@ using the argument show_errplot = TRUE." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
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<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
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- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
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+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
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<h1>Function to plot squared residuals and the error model for an mkin object</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrplot.R" class="external-link"><code>R/mkinerrplot.R</code></a></small>
<div class="hidden name"><code>mkinerrplot.Rd</code></div>
</div>
@@ -151,128 +96,133 @@ using the argument show_errplot = TRUE." />
<p>This function plots the squared residuals for the specified subset of the
observed variables from an mkinfit object. In addition, one or more dashed
line(s) show the fitted error model. A combined plot of the fitted model
-and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
+and this error model plot can be obtained with <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>
using the argument <code>show_errplot = TRUE</code>.</p>
</div>
- <pre class="usage"><span class='fu'>mkinerrplot</span><span class='op'>(</span>
- <span class='va'>object</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'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
- xlim <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='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>predicted</span><span class='op'>)</span><span class='op'>)</span>,
- xlab <span class='op'>=</span> <span class='st'>"Predicted"</span>,
- ylab <span class='op'>=</span> <span class='st'>"Squared residual"</span>,
- maxy <span class='op'>=</span> <span class='st'>"auto"</span>,
- legend <span class='op'>=</span> <span class='cn'>TRUE</span>,
- lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
- col_obs <span class='op'>=</span> <span class='st'>"auto"</span>,
- pch_obs <span class='op'>=</span> <span class='st'>"auto"</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>object</th>
- <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td>
- </tr>
- <tr>
- <th>obs_vars</th>
- <td><p>A character vector of names of the observed variables for
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrplot</span><span class="op">(</span></span>
+<span> <span class="va">object</span>,</span>
+<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
+<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">predicted</span><span class="op">)</span><span class="op">)</span>,</span>
+<span> xlab <span class="op">=</span> <span class="st">"Predicted"</span>,</span>
+<span> ylab <span class="op">=</span> <span class="st">"Squared residual"</span>,</span>
+<span> maxy <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span>
+<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd>
+
+
+<dt>obs_vars</dt>
+<dd><p>A character vector of names of the observed variables for
which residuals should be plotted. Defaults to all observed variables in
-the model</p></td>
- </tr>
- <tr>
- <th>xlim</th>
- <td><p>plot range in x direction.</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>maxy</th>
- <td><p>Maximum value of the residuals. This is used for the scaling of
-the y axis and defaults to "auto".</p></td>
- </tr>
- <tr>
- <th>legend</th>
- <td><p>Should a legend be plotted?</p></td>
- </tr>
- <tr>
- <th>lpos</th>
- <td><p>Where should the legend be placed? Default is "topright". Will
-be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td>
- </tr>
- <tr>
- <th>col_obs</th>
- <td><p>Colors for the observed variables.</p></td>
- </tr>
- <tr>
- <th>pch_obs</th>
- <td><p>Symbols to be used for the observed variables.</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>Nothing is returned by this function, as it is called for its side
-effect, namely to produce a plot.</p>
- <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+the model</p></dd>
- <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted
-lines of the mkinfit object.</p></div>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
- <p>Johannes Ranke</p>
+<dt>xlim</dt>
+<dd><p>plot range in x direction.</p></dd>
+
+
+<dt>xlab</dt>
+<dd><p>Label for the x axis.</p></dd>
+
+
+<dt>ylab</dt>
+<dd><p>Label for the y axis.</p></dd>
+
+
+<dt>maxy</dt>
+<dd><p>Maximum value of the residuals. This is used for the scaling of
+the y axis and defaults to "auto".</p></dd>
+
+
+<dt>legend</dt>
+<dd><p>Should a legend be plotted?</p></dd>
+
+
+<dt>lpos</dt>
+<dd><p>Where should the legend be placed? Default is "topright". Will
+be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd>
+
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='co'># \dontrun{</span>
-<span class='va'>model</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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+<dt>col_obs</dt>
+<dd><p>Colors for the observed variables.</p></dd>
-</div></pre>
+
+<dt>pch_obs</dt>
+<dd><p>Symbols to be used for the observed variables.</p></dd>
+
+
+<dt>frame</dt>
+<dd><p>Should a frame be drawn around the plots?</p></dd>
+
+
+<dt>...</dt>
+<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>Nothing is returned by this function, as it is called for its side
+effect, namely to produce a plot.</p>
+ </div>
+ <div id="see-also">
+ <h2>See also</h2>
+ <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted
+lines of the mkinfit object.</p></div>
+ </div>
+ <div id="author">
+ <h2>Author</h2>
+ <p>Johannes Ranke</p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">model</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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
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