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-rw-r--r--docs/reference/mmkin.html91
1 files changed, 48 insertions, 43 deletions
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 67397827..fe10c88f 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mmkin • mkin</title>
+<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title>
<!-- jquery -->
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@@ -26,12 +25,14 @@
<script src="../pkgdown.js"></script>
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-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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+
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<body>
@@ -71,6 +72,9 @@
<li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
</ul>
</li>
<li>
@@ -96,8 +100,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1>
</div>
@@ -105,37 +108,38 @@
specified in its first two arguments.</p>
- <pre><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>,
+ <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>,
<span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <dl class="dl-horizontal">
- <dt>models</dt>
- <dd>
- Either a character vector of shorthand names (&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;,
- &quot;HS&quot;, &quot;SFORB&quot;), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code>
- objects.
- </dd>
- <dt>datasets</dt>
- <dd>
- An optionally named list of datasets suitable as observed data for
- <code><a href='mkinfit.html'>mkinfit</a></code>.
- </dd>
- <dt>cores</dt>
- <dd>
- The number of cores to be used for multicore processing. This is only
- used when the <code>cluster</code> argument is <code>NULL</code>.
- </dd>
- <dt>cluster</dt>
- <dd>
- A cluster as returned by <code>makeCluster</code> to be used for parallel
- execution.
- </dd>
- <dt>&#8230;</dt>
- <dd>
- Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.
- </dd>
- </dl>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>models</th>
+ <td><p>Either a character vector of shorthand names ("SFO", "FOMC", "DFOP",
+ "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code>
+ objects.</p></td>
+ </tr>
+ <tr>
+ <th>datasets</th>
+ <td><p>An optionally named list of datasets suitable as observed data for
+ <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>cores</th>
+ <td><p>The number of cores to be used for multicore processing. This is only
+ used when the <code>cluster</code> argument is <code>NULL</code>.</p></td>
+ </tr>
+ <tr>
+ <th>cluster</th>
+ <td><p>A cluster as returned by <code>makeCluster</code> to be used for parallel
+ execution.</p></td>
+ </tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ </tr>
+ </table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -144,7 +148,7 @@
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p>
+ <p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -160,11 +164,12 @@
<span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'>&lt;-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
-<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
-
+<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
+#&gt; <span class='warning'>Convergence code is 1</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
+#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'>
<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 16.360 0.128 9.017 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 21.888 0.004 21.892 </div><div class='input'>
+#&gt; 16.092 0.132 11.761 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 25.004 0.000 25.000 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340479 0.2659521 0.7505687 0.2494313
@@ -174,17 +179,17 @@
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
-#&gt; parent 0.8777688 2.915885
+#&gt; parent 0.8777689 2.915885
#&gt; M1 2.3257456 7.725960
-#&gt; M2 33.7200881 112.015708
+#&gt; M2 33.7200862 112.015702
#&gt; </div><div class='input'>
<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-12.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-15.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-17.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-19.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
<span class='co'># by plot.mkinfit and can be plotted using plot_sep</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])
+<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-21.png' alt='' width='540' height='400' /><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])
<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
<span class='co'># allow to plot the observed variables separately</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-23.png' alt='' width='540' height='400' /><div class='input'>
</div></pre>
</div>
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