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diff --git a/docs/mccall81_245T.html b/docs/mccall81_245T.html deleted file mode 100644 index 426a35c4..00000000 --- a/docs/mccall81_245T.html +++ /dev/null @@ -1,232 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>mccall81_245T. mkin 0.9.44.9000</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="index.html">mkin 0.9.44.9000</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</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><span class="symbol">mccall81_245T</span></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'> <span class="symbol">SFO_SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">T245</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"phenol"</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">phenol</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"anisole"</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">anisole</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div> -<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> -<div class='input'> <span class="comment">## Not run: ------------------------------------</span> -<span class="comment"># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> -<span class="comment"># summary(fit.1, data = FALSE)</span> -<span class="comment"># </span> -<span class="comment">## ---------------------------------------------</span> - <span class="comment"># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> - <span class="symbol">fit.2</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO_SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span><span class="keyword">(</span><span class="symbol">mccall81_245T</span><span class="keyword">,</span> <span class="symbol">soil</span> == <span class="string">"Commerce"</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">parms.ini</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_phenol_sink</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">fixed_parms</span> <span class="argument">=</span> <span class="string">"k_phenol_sink"</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span> - <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="symbol">fit.2</span><span class="keyword">,</span> <span class="argument">data</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></div> -<div class='output'>mkin version: 0.9.44.9000 -R version: 3.3.1 -Date of fit: Sat Sep 10 05:53:00 2016 -Date of summary: Sat Sep 10 05:53:00 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 1.45 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></pre> - </div> - <div class="span4 sidebar"> - <!-- <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>. 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