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-rw-r--r--docs/reference/test_data_from_UBA_2014.html109
1 files changed, 53 insertions, 56 deletions
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 0040c331..237149a5 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -10,23 +10,27 @@
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@@ -38,7 +42,6 @@
<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" />
<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation
software packages (Ranke, 2014)." />
-<meta name="twitter:card" content="summary" />
@@ -56,7 +59,7 @@
</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">
@@ -70,7 +73,7 @@
</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>
@@ -114,7 +117,12 @@
</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 -->
@@ -144,7 +152,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>.
- Each dataset has, among others, the following components</p><dl class='dl-horizontal'>
+ Each dataset has, among others, the following components</p><dl'>
<dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd>
<dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
@@ -165,23 +173,16 @@
<span class='co'># model).</span>
<span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
<span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
-#&gt; parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
-#&gt; k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
-#&gt; k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
-#&gt; k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
-#&gt; k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
-#&gt; sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
-#&gt; Lower Upper
-#&gt; parent_w_0 91.48420503 100.4871438
-#&gt; k_parent_w_sink 0.30668904 0.4234571
-#&gt; k_parent_w_parent_s 0.03423904 0.1062455
-#&gt; k_parent_s_sink 0.00000000 Inf
-#&gt; k_parent_s_parent_w 0.02289956 0.2404043
-#&gt; sigma 2.00184022 3.9639169</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
-#&gt; All data 0.09246946 5 6
-#&gt; parent_w 0.06377096 3 3
-#&gt; parent_s 0.20882325 2 3</div><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_w_0 95.91998116 NA NA NA NA NA
+#&gt; k_parent_w 0.41145375 NA NA NA NA NA
+#&gt; k_parent_s 0.04663944 NA NA NA NA NA
+#&gt; f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA
+#&gt; f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA
+#&gt; sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.1090929 5 6
+#&gt; parent_w 0.0817436 3 3
+#&gt; parent_s 0.1619965 2 3</div><div class='input'>
<span class='co'># This is the evaluation used for the validation of software packages</span>
<span class='co'># in the expertise from 2014</span>
<span class='no'>m_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
@@ -190,42 +191,38 @@
<span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</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: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
-#&gt; k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582
-#&gt; k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803
-#&gt; k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807
-#&gt; k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463
-#&gt; f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA
-#&gt; f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA
-#&gt; f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937
-#&gt; f_M2_to_M3 0.55641331 0.595125445 0.9349513 1.807725e-01 0.008003317
+#&gt; parent_0 76.55425585 0.859186419 89.1008682 1.113862e-26 74.755958727
+#&gt; k_parent 0.12081956 0.004601919 26.2541704 1.077361e-16 0.111561576
+#&gt; k_M1 0.84258631 0.806165101 1.0451783 1.545282e-01 0.113778787
+#&gt; k_M2 0.04210878 0.017083048 2.4649453 1.170195e-02 0.018013823
+#&gt; k_M3 0.01122919 0.007245869 1.5497365 6.885076e-02 0.002909418
+#&gt; f_parent_to_M1 0.32240194 0.240785506 1.3389591 9.819219e-02 NA
+#&gt; f_parent_to_M2 0.16099854 0.033691990 4.7785405 6.531222e-05 NA
+#&gt; f_M1_to_M3 0.27921506 0.269425556 1.0363347 1.565282e-01 0.022977927
+#&gt; f_M2_to_M3 0.55641328 0.595121733 0.9349571 1.807710e-01 0.008002321
#&gt; sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
#&gt; Upper
-#&gt; parent_0 78.35255192
+#&gt; parent_0 78.35255298
#&gt; k_parent 0.13084582
-#&gt; k_M1 6.23641265
-#&gt; k_M2 0.09843279
-#&gt; k_M3 0.04333950
+#&gt; k_M1 6.23975442
+#&gt; k_M2 0.09843270
+#&gt; k_M3 0.04334016
#&gt; f_parent_to_M1 NA
#&gt; f_parent_to_M2 NA
-#&gt; f_M1_to_M3 0.86443083
-#&gt; f_M2_to_M3 0.99489847
+#&gt; f_M1_to_M3 0.86450919
+#&gt; f_M2_to_M3 0.99489910
#&gt; sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
#&gt; All data 0.09649963 9 20
#&gt; parent 0.04721283 2 6
-#&gt; M1 0.26551209 2 5
+#&gt; M1 0.26551208 2 5
#&gt; M2 0.20327575 2 5
-#&gt; M3 0.05196549 3 4</div><div class='input'> # }
+#&gt; M3 0.05196550 3 4</div><div class='input'> # }
</div></pre>
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- <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="#source">Source</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>
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@@ -236,7 +233,7 @@
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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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