aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/mccall81_245T.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/reference/mccall81_245T.html')
-rw-r--r--docs/reference/mccall81_245T.html246
1 files changed, 246 insertions, 0 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
new file mode 100644
index 00000000..74b9c088
--- /dev/null
+++ b/docs/reference/mccall81_245T.html
@@ -0,0 +1,246 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <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>
+ — mccall81_245T • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
+ 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
+ extracts.</p>
+
+
+ <pre><span class='no'>mccall81_245T</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A dataframe containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as
+ an acronym for 2,4,5-T. T245 is a legitimate object name
+ in R, which is necessary for specifying models using
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</dd>
+ <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
+ treatment</dd>
+ <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
+ <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
+ <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
+ <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
+ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
+<span class='co'># summary(fit.1, data = FALSE)</span>
+<span class='co'># </span>
+<span class='co'>## ---------------------------------------------</span>
+ <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span>
+ <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
+ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Wed Oct 26 23:50:40 2016
+#&gt; Date of summary: Wed Oct 26 23:50:40 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
+#&gt; d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#&gt; k_phenol_anisole * phenol
+#&gt; d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 246 model solutions performed in 1.43 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; T245_0 100.9000 state
+#&gt; k_T245_sink 0.1000 deparm
+#&gt; k_T245_phenol 0.1001 deparm
+#&gt; k_phenol_anisole 0.1002 deparm
+#&gt; k_anisole_sink 0.1003 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; T245_0 100.900000 -Inf Inf
+#&gt; log_k_T245_sink -2.302585 -Inf Inf
+#&gt; log_k_T245_phenol -2.301586 -Inf Inf
+#&gt; log_k_phenol_anisole -2.300587 -Inf Inf
+#&gt; log_k_anisole_sink -2.299590 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; phenol_0 0 state
+#&gt; anisole_0 0 state
+#&gt; k_phenol_sink 0 deparm
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; T245_0 103.9000 2.35200 98.930 108.8000
+#&gt; log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
+#&gt; log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
+#&gt; log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
+#&gt; log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
+#&gt;
+#&gt; Parameter correlation:
+#&gt; T245_0 log_k_T245_sink log_k_T245_phenol
+#&gt; T245_0 1.00000 0.63761 -0.1742
+#&gt; log_k_T245_sink 0.63761 1.00000 -0.3831
+#&gt; log_k_T245_phenol -0.17416 -0.38313 1.0000
+#&gt; log_k_phenol_anisole -0.05948 0.08745 -0.3047
+#&gt; log_k_anisole_sink -0.16208 -0.60469 0.5227
+#&gt; log_k_phenol_anisole log_k_anisole_sink
+#&gt; T245_0 -0.05948 -0.1621
+#&gt; log_k_T245_sink 0.08745 -0.6047
+#&gt; log_k_T245_phenol -0.30470 0.5227
+#&gt; log_k_phenol_anisole 1.00000 -0.1774
+#&gt; log_k_anisole_sink -0.17744 1.0000
+#&gt;
+#&gt; Residual standard error: 2.706 on 19 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000
+#&gt; k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
+#&gt; k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
+#&gt; k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
+#&gt; k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 9.831 5 17
+#&gt; T245 7.908 3 5
+#&gt; phenol 99.808 1 6
+#&gt; anisole 5.379 1 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; T245_sink 0.3772
+#&gt; T245_phenol 0.6228
+#&gt; phenol_anisole 1.0000
+#&gt; phenol_sink 0.0000
+#&gt; anisole_sink 1.0000
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; T245 15.982 53.091
+#&gt; phenol 1.711 5.685
+#&gt; anisole 103.784 344.763
+#&gt; </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="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>

Contact - Imprint