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diff --git a/docs/mccall81_245T.html b/docs/mccall81_245T.html new file mode 100644 index 00000000..426a35c4 --- /dev/null +++ b/docs/mccall81_245T.html @@ -0,0 +1,232 @@ +<!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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