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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 --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- 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'><-</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'>#> <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'>#> <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'><-</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'>#> mkin version: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:14:14 2017 -#> Date of summary: Sat Jul 29 15:14:14 2017 -#> -#> 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 612 model solutions performed in 3.558 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 -26.8400 NA NA NA -#> log_k_phenol_anisole -0.9037 NA NA NA -#> log_k_anisole_sink -5.0090 NA NA NA -#> -#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> 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 7.499e-02 NA NA -#> k_phenol_sink 2.212e-12 7.870e-12 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 5.462e-12 -#> 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='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'><-</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'>#> mkin version: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:14:15 2017 -#> 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'>#> mkin version used for fitting: 0.9.47.1 +#> R version used for fitting: 3.4.3 +#> Date of fit: Thu Mar 1 14:26:15 2018 +#> Date of summary: Thu Mar 1 14:26:15 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -238,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.431 s +#> Fitted with method Port using 246 model solutions performed in 1.359 s #> #> Weighting: none #> @@ -340,7 +264,7 @@ </div> <div class="pkgdown"> - <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> </div> </footer> |