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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-12 16:34:00 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-12 16:34:00 +0200
commit6211f3ef4995657798686d8d4ab43ed9406e8a08 (patch)
tree4be80cf595880876d51c9cb85f07464b99bc8c83 /docs/reference/schaefer07_complex_case.html
parentc7fcc2f8af47e95cf6164c00a4902340624c13dc (diff)
Update vignettes and docs
Diffstat (limited to 'docs/reference/schaefer07_complex_case.html')
-rw-r--r--docs/reference/schaefer07_complex_case.html63
1 files changed, 32 insertions, 31 deletions
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 27b19430..dcecc9b5 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -10,23 +10,27 @@
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -39,7 +43,6 @@
<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the
software quality of KinGUI in the original publication (Schäfer et al., 2007).
The results from the fitting are also included." />
-<meta name="twitter:card" content="summary" />
@@ -57,7 +60,7 @@
</head>
- <body>
+ <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -71,7 +74,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
</span>
</div>
@@ -115,7 +118,12 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin/">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
@@ -145,7 +153,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
- <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl class='dl-horizontal'>
+ <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl'>
<dt><code>time</code></dt><dd><p>a numeric vector</p></dd>
<dt><code>parent</code></dt><dd><p>a numeric vector</p></dd>
<dt><code>A1</code></dt><dd><p>a numeric vector</p></dd>
@@ -170,20 +178,17 @@
<span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># \dontrun{</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+ <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink
-#&gt; 0.3809619 0.1954667 0.4235714 0.0000000 0.4479620 0.5520380
-#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
+#&gt; 0.3809618 0.1954667 0.4235715 0.0000000 0.4479625 0.5520375
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 13.95078 46.34350
-#&gt; A1 49.75344 165.27737
-#&gt; B1 37.26907 123.80517
-#&gt; C1 11.23131 37.30960
-#&gt; A2 28.50627 94.69577
+#&gt; A1 49.75346 165.27741
+#&gt; B1 37.26904 123.80508
+#&gt; C1 11.23130 37.30958
+#&gt; A2 28.50628 94.69580
#&gt; </div><div class='input'> <span class='co'># }</span>
<span class='co'># Compare with the results obtained in the original publication</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt; compound parameter KinGUI ModelMaker deviation
@@ -202,14 +207,10 @@
#&gt; 13 metabolite A2 degradation rate 0.0245 0.0244 0.4
#&gt; 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre>
</div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
- <h2>Contents</h2>
- <ul class="nav nav-pills nav-stacked">
- <li><a href="#format">Format</a></li>
- <li><a href="#references">References</a></li>
- <li><a href="#examples">Examples</a></li>
- </ul>
-
+ <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>
@@ -220,7 +221,7 @@
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<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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