<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> <link 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recovered in diethylether extracts." /> <meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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" aria-expanded="false"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </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">0.9.48.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> <li> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> <a href="../articles/web_only/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> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> </ul> </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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> <div class="hidden name"><code>mccall81_245T.Rd</code></div> </div> <div class="ref-description"> <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> </div> <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.</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>.</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> <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'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 #> Date of fit: Mon Mar 4 10:08:00 2019 #> Date of summary: Mon Mar 4 10:08:00 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 #> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - #> k_phenol_anisole * phenol #> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole #> #> Model predictions using solution type deSolve #> #> Fitted with method Port using 574 model solutions performed in 3.762 s #> #> Weighting: none #> #> Starting values for parameters to be optimised: #> value type #> T245_0 100.9000 state #> k_T245_sink 0.1000 deparm #> k_T245_phenol 0.1001 deparm #> k_phenol_sink 0.1002 deparm #> k_phenol_anisole 0.1003 deparm #> k_anisole_sink 0.1004 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> T245_0 100.900000 -Inf Inf #> log_k_T245_sink -2.302585 -Inf Inf #> log_k_T245_phenol -2.301586 -Inf Inf #> log_k_phenol_sink -2.300587 -Inf Inf #> log_k_phenol_anisole -2.299590 -Inf Inf #> log_k_anisole_sink -2.298593 -Inf Inf #> #> Fixed parameter values: #> value type #> phenol_0 0 state #> anisole_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> T245_0 103.9000 NA NA NA #> log_k_T245_sink -4.1130 NA NA NA #> log_k_T245_phenol -3.6120 NA NA NA #> log_k_phenol_sink -25.0800 NA NA NA #> log_k_phenol_anisole -0.9037 NA NA NA #> log_k_anisole_sink -5.0090 NA NA NA #> #> Parameter correlation: #> Could not estimate covariance matrix; singular system. #> Residual standard error: 2.78 on 18 degrees of freedom #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA #> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA #> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA #> k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA #> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA #> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA #> #> Chi2 error levels in percent: #> err.min n.optim df #> All data 10.070 6 16 #> T245 7.908 3 5 #> phenol 106.445 2 5 #> anisole 5.379 1 6 #> #> Resulting formation fractions: #> ff #> T245_sink 3.772e-01 #> T245_phenol 6.228e-01 #> phenol_sink 3.175e-11 #> phenol_anisole 1.000e+00 #> anisole_sink 1.000e+00 #> #> Estimated disappearance times: #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 #> anisole 103.784 344.763</div><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'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 #> Date of fit: Mon Mar 4 10:08:02 2019 #> Date of summary: Mon Mar 4 10:08:02 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 #> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - #> k_phenol_anisole * phenol #> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole #> #> Model predictions using solution type deSolve #> #> Fitted with method Port using 246 model solutions performed in 1.598 s #> #> Weighting: none #> #> Starting values for parameters to be optimised: #> value type #> T245_0 100.9000 state #> k_T245_sink 0.1000 deparm #> k_T245_phenol 0.1001 deparm #> k_phenol_anisole 0.1002 deparm #> k_anisole_sink 0.1003 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> T245_0 100.900000 -Inf Inf #> log_k_T245_sink -2.302585 -Inf Inf #> log_k_T245_phenol -2.301586 -Inf Inf #> log_k_phenol_anisole -2.300587 -Inf Inf #> log_k_anisole_sink -2.299590 -Inf Inf #> #> Fixed parameter values: #> value type #> phenol_0 0 state #> anisole_0 0 state #> k_phenol_sink 0 deparm #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> T245_0 103.9000 2.35200 98.930 108.8000 #> log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350 #> log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070 #> log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637 #> log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750 #> #> Parameter correlation: #> T245_0 log_k_T245_sink log_k_T245_phenol #> T245_0 1.00000 0.63761 -0.1742 #> log_k_T245_sink 0.63761 1.00000 -0.3831 #> log_k_T245_phenol -0.17416 -0.38313 1.0000 #> log_k_phenol_anisole -0.05948 0.08745 -0.3047 #> log_k_anisole_sink -0.16208 -0.60469 0.5227 #> log_k_phenol_anisole log_k_anisole_sink #> T245_0 -0.05948 -0.1621 #> log_k_T245_sink 0.08745 -0.6047 #> log_k_T245_phenol -0.30470 0.5227 #> log_k_phenol_anisole 1.00000 -0.1774 #> log_k_anisole_sink -0.17744 1.0000 #> #> Residual standard error: 2.706 on 19 degrees of freedom #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000 #> k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159 #> k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999 #> k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820 #> k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844 #> #> Chi2 error levels in percent: #> err.min n.optim df #> All data 9.831 5 17 #> T245 7.908 3 5 #> phenol 99.808 1 6 #> anisole 5.379 1 6 #> #> Resulting formation fractions: #> ff #> T245_sink 0.3772 #> T245_phenol 0.6228 #> phenol_anisole 1.0000 #> phenol_sink 0.0000 #> anisole_sink 1.0000 #> #> Estimated disappearance times: #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 #> anisole 103.784 344.763</div><div class='input'> </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.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> </div> </footer> </div> </body> </html>