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diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 4fa32b30..9a681191 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ <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> +<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -26,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -71,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -96,8 +100,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> </div> @@ -106,21 +109,20 @@ extracts.</p> - <pre><span class='no'>mccall81_245T</span></pre> + <pre class="usage"><span class='no'>mccall81_245T</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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 + <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'> + <dt><code>name</code></dt><dd><p>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> - <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> + <code><a href='mkinmod.html'>mkinmod</a></code>.</p></dd> + <dt><code>time</code></dt><dd><p>a numeric vector containing sampling times in days after + treatment</p></dd> + <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> + <dt><code>soil</code></dt><dd><p>a factor containing the name of the soil</p></dd> + </dl> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> @@ -132,16 +134,11 @@ <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='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>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> -#> <span class='warning'>Convergence code is 1</span></div><div class='input'> <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: 0.9.45.1 -#> R version: 3.3.3 -#> Date of fit: Wed Mar 15 09:44:52 2017 -#> Date of summary: Wed Mar 15 09:44:52 2017 -#> -#> -#> Warning: Optimisation by method Port did not converge. -#> Convergence code is 1 -#> + <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: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:45:02 2017 +#> Date of summary: Fri May 5 12:45:02 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -151,7 +148,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 590 model solutions performed in 3.519 s +#> Fitted with method Port using 612 model solutions performed in 3.576 s #> #> Weighting: none #> @@ -183,7 +180,7 @@ #> 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 -26.3900 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 #> @@ -198,8 +195,8 @@ #> 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 7.498e-02 NA NA -#> k_phenol_sink 3.457e-12 1.230e-11 5.000e-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 #> @@ -214,7 +211,7 @@ #> ff #> T245_sink 3.772e-01 #> T245_phenol 6.228e-01 -#> phenol_sink 8.534e-12 +#> phenol_sink 5.462e-12 #> phenol_anisole 1.000e+00 #> anisole_sink 1.000e+00 #> @@ -228,10 +225,10 @@ <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: 0.9.45.1 -#> R version: 3.3.3 -#> Date of fit: Wed Mar 15 09:44:54 2017 -#> Date of summary: Wed Mar 15 09:44:54 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: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:45:04 2017 +#> Date of summary: Fri May 5 12:45:04 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -241,7 +238,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.449 s +#> Fitted with method Port using 246 model solutions performed in 1.461 s #> #> Weighting: none #> |