aboutsummaryrefslogblamecommitdiff
path: root/inst/web/mccall81_245T.html
blob: 335af648476e8fbd49c4c783664e6b57c3c49936 (plain) (tree)
1
2
3
4
5



                          
                                              




























                                                                                      
                                                    














































































                                                                                                                                                                                     
                                                 
                       

                                          







                                                                                      
                                                                      






























































































                                                                                                                                                       
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
<title>mccall81_245T. mkin 0.9.43.9000</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="">

<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">

<!--[if lt IE 9]>
  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    }
  });
</script>
<script type="text/javascript"
  src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
  </head>

  <body>
    <div class="navbar">
  <div class="navbar-inner">
    <div class="container">
      <a class="brand" href="#">mkin 0.9.43.9000</a>
      <div class="nav">
        <ul class="nav">
          <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
        </ul>
      </div>
    </div>
  </div>
</div>

    <div class="container">
      <header>
        
      </header>
      
      <h1>
  Datasets on aerobic soil metabolism of 2,4,5-T in six soils
</h1>

<div class="row">
  <div class="span8">
    <h2>Usage</h2>
    <pre><div>mccall81_245T</div></pre>
        
    <div class="Description">
      <h2>Description</h2>

      <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>

    <div class="Format">
      <h2>Format</h2>

      <p>A dataframe containing the following variables.
  <dl>
    <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></p>
  
      <p><dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
                       treatment</dd></p>
  
      <p><dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd></p>
  
      <p><dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd></p>
  
      <p></dl></p>
  
      <p></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'>  SFO_SFO_SFO &lt;- mkinmod(T245 = list(type = &quot;SFO&quot;, to = &quot;phenol&quot;),
                         phenol = list(type = &quot;SFO&quot;, to = &quot;anisole&quot;),
                         anisole = list(type = &quot;SFO&quot;))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'>  ## Not run: 
#     fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == &quot;Commerce&quot;))
#     summary(fit.1, data = FALSE)
#   ## End(Not run)
  # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero
  fit.2 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == &quot;Commerce&quot;),
                 parms.ini = c(k_phenol_sink = 0),
                 fixed_parms = &quot;k_phenol_sink&quot;, quiet = TRUE)
  summary(fit.2, data = FALSE)
</div>
<div class='output'>mkin version:    0.9.43.9000 
R version:       3.3.1 
Date of fit:     Tue Jun 28 08:14:29 2016 
Date of summary: Tue Jun 28 08:14:29 2016 

Equations:
d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - k_phenol_anisole * phenol
d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole

Model predictions using solution type deSolve 

Fitted with method Port using 246 model solutions performed in 3.812 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 log_k_phenol_anisole log_k_anisole_sink
T245_0                1.00000         0.63761           -0.1742             -0.05948            -0.1621
log_k_T245_sink       0.63761         1.00000           -0.3831              0.08745            -0.6047
log_k_T245_phenol    -0.17416        -0.38313            1.0000             -0.30470             0.5227
log_k_phenol_anisole -0.05948         0.08745           -0.3047              1.00000            -0.1774
log_k_anisole_sink   -0.16208        -0.60469            0.5227             -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(&gt;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></pre>
  </div>
  <div class="span4">
    <!-- <ul>
      <li>mccall81_245T</li>
    </ul>
    <ul>
      <li>datasets</li>
    </ul> -->
      
        
  </div>
</div>
      
      <footer>
      <p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
      </footer>
    </div>
  </body>
</html>

Contact - Imprint