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.html67
1 files changed, 32 insertions, 35 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 4fa32b30..9a681191 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.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>
- — mccall81_245T • mkin</title>
+<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -26,12 +25,14 @@
<script src="../pkgdown.js"></script>
<!-- mathjax -->
-<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>
<!--[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>
@@ -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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
</div>
@@ -106,21 +109,20 @@
extracts.</p>
- <pre><span class='no'>mccall81_245T</span></pre>
+ <pre class="usage"><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
+ <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd><p>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>
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</p></dd>
+ <dt><code>time</code></dt><dd><p>a numeric vector containing sampling times in days after
+ treatment</p></dd>
+ <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd>
+ <dt><code>soil</code></dt><dd><p>a factor containing the name of the soil</p></dd>
+ </dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@@ -132,16 +134,11 @@
<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 co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
- <span class='no'>fit.1</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'>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='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.1
-#&gt; R version: 3.3.3
-#&gt; Date of fit: Wed Mar 15 09:44:52 2017
-#&gt; Date of summary: Wed Mar 15 09:44:52 2017
-#&gt;
-#&gt;
-#&gt; Warning: Optimisation by method Port did not converge.
-#&gt; Convergence code is 1
-#&gt;
+ <span class='no'>fit.1</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
+#&gt; R version: 3.4.0
+#&gt; Date of fit: Fri May 5 12:45:02 2017
+#&gt; Date of summary: Fri May 5 12:45:02 2017
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -151,7 +148,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 590 model solutions performed in 3.519 s
+#&gt; Fitted with method Port using 612 model solutions performed in 3.576 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -183,7 +180,7 @@
#&gt; T245_0 103.9000 NA NA NA
#&gt; log_k_T245_sink -4.1130 NA NA NA
#&gt; log_k_T245_phenol -3.6120 NA NA NA
-#&gt; log_k_phenol_sink -26.3900 NA NA NA
+#&gt; log_k_phenol_sink -26.8400 NA NA NA
#&gt; log_k_phenol_anisole -0.9037 NA NA NA
#&gt; log_k_anisole_sink -5.0090 NA NA NA
#&gt;
@@ -198,8 +195,8 @@
#&gt; Estimate t value Pr(&gt;t) Lower Upper
#&gt; T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA
#&gt; k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA
-#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA
-#&gt; k_phenol_sink 3.457e-12 1.230e-11 5.000e-01 NA NA
+#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.499e-02 NA NA
+#&gt; k_phenol_sink 2.212e-12 7.870e-12 5.000e-01 NA NA
#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA
#&gt; k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA
#&gt;
@@ -214,7 +211,7 @@
#&gt; ff
#&gt; T245_sink 3.772e-01
#&gt; T245_phenol 6.228e-01
-#&gt; phenol_sink 8.534e-12
+#&gt; phenol_sink 5.462e-12
#&gt; phenol_anisole 1.000e+00
#&gt; anisole_sink 1.000e+00
#&gt;
@@ -228,10 +225,10 @@
<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: 0.9.45.1
-#&gt; R version: 3.3.3
-#&gt; Date of fit: Wed Mar 15 09:44:54 2017
-#&gt; Date of summary: Wed Mar 15 09:44:54 2017
+ <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: 0.9.45.2
+#&gt; R version: 3.4.0
+#&gt; Date of fit: Fri May 5 12:45:04 2017
+#&gt; Date of summary: Fri May 5 12:45:04 2017
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -241,7 +238,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.449 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.461 s
#&gt;
#&gt; Weighting: none
#&gt;

Contact - Imprint