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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
commit5aec8e34680e05671347f7577ae36c9ad8e37063 (patch)
tree2cfc0f696cc202e9c9a7b7951930bfe88c355d23 /docs/reference/mccall81_245T.html
parent7ceb1dc732ac8674dd8dd70b798fe12378ec10af (diff)
parent8650f26f63a64ac8b72326e2679719744ac99f07 (diff)
Merge branch 'master' of kolab:mkin
Diffstat (limited to 'docs/reference/mccall81_245T.html')
-rw-r--r--docs/reference/mccall81_245T.html124
1 files changed, 24 insertions, 100 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 0111deb3..ec7f8ccd 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -18,12 +18,21 @@
<!-- 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">
+<!-- clipboard.js -->
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" />
+<meta property="og:description" content="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." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +79,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +95,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -127,108 +134,25 @@
<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>
+ <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 co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <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'> </div><span class='co'># NOT RUN {</span>
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:14 2017
-#&gt; Date of summary: Sat Jul 29 15:14:14 2017
-#&gt;
-#&gt; Equations:
-#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#&gt; k_phenol_anisole * phenol
-#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 612 model solutions performed in 3.558 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_sink 0.1002 deparm
-#&gt; k_phenol_anisole 0.1003 deparm
-#&gt; k_anisole_sink 0.1004 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_sink -2.300587 -Inf Inf
-#&gt; log_k_phenol_anisole -2.299590 -Inf Inf
-#&gt; log_k_anisole_sink -2.298593 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; phenol_0 0 state
-#&gt; anisole_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&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 -26.8400 NA NA NA
-#&gt; log_k_phenol_anisole -0.9037 NA NA NA
-#&gt; log_k_anisole_sink -5.0090 NA NA NA
-#&gt;
-#&gt; Parameter correlation:</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#&gt; Could not estimate covariance matrix; singular system:
-#&gt;
-#&gt; Residual standard error: 2.78 on 18 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 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 7.499e-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;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 10.070 6 16
-#&gt; T245 7.908 3 5
-#&gt; phenol 106.445 2 5
-#&gt; anisole 5.379 1 6
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; T245_sink 3.772e-01
-#&gt; T245_phenol 6.228e-01
-#&gt; phenol_sink 5.462e-12
-#&gt; phenol_anisole 1.000e+00
-#&gt; anisole_sink 1.000e+00
-#&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</div><div class='input'>
- <span class='co'># No convergence, no covariance matrix ...</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>)
+
+<span class='co'># }</span><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span>
<span class='co'># 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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:15 2017
-#&gt; Date of summary: Sat Jul 29 15:14:15 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 used for fitting: 0.9.47.1
+#&gt; R version used for fitting: 3.4.3
+#&gt; Date of fit: Thu Mar 1 14:26:15 2018
+#&gt; Date of summary: Thu Mar 1 14:26:15 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -238,7 +162,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.431 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.359 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -340,7 +264,7 @@
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- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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