aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/mccall81_245T.html
blob: 17e900a4aca238f22f9ab4ceffd2eee9d82880fa (plain) (tree)



























































































































                                                                                                                                                                                                                                                                                                                                                                                                                                                   

                                                








                                                                        
                                                                            




























































































                                                                                                                                            
<!-- 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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="../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">
      <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="../index.html">Home</a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
      </ul>
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/jranke/mkin">
    <span class="fa fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->
      
      </header>

      <div class="page-header">
  <h1>
</h1>
</div>

<div class="row">
  <div class="col-md-9">
    
    <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>
        
    <div class="Format">
      <h2>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>mkinmod</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>
    </div>

    <div class="Source">
      <h2>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>
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'>  <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</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'>mkinfit</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:     Thu Oct  6 09:39:12 2016 
#&gt; Date of summary: Thu Oct  6 09:39:12 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 1.544 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">
  </div>
</div>

      <footer>
      <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p>
      </footer>
   </div>

  </body>
</html>

Contact - Imprint