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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/mccall81_245T.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/mccall81_245T.html')
| -rw-r--r-- | docs/dev/reference/mccall81_245T.html | 245 |
1 files changed, 245 insertions, 0 deletions
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evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/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> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> + + <div class="hidden name"><code>mccall81_245T.Rd</code></div> + </div> + + <div class="ref-description"> + <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> + + <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.</p><dl'> + <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>.</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> + + <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 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> + + <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'><a href='https://rdrr.io/r/base/list.html'>list</a></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'><a href='https://rdrr.io/r/base/list.html'>list</a></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'><a href='https://rdrr.io/r/base/list.html'>list</a></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='co'># \dontrun{</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'><a href='https://rdrr.io/r/base/subset.html'>subset</a></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: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) +#> T245_0 1.038550e+02 2.184707509 47.537272 4.472189e-18 +#> k_T245 4.337042e-02 0.001898397 22.845818 2.276912e-13 +#> k_phenol 4.050581e-01 0.298699410 1.356073 9.756993e-02 +#> k_anisole 6.678742e-03 0.000802144 8.326114 2.623179e-07 +#> f_T245_to_phenol 6.227599e-01 0.398534147 1.562626 6.949418e-02 +#> f_phenol_to_anisole 1.000000e+00 0.671844135 1.488440 7.867793e-02 +#> sigma 2.514628e+00 0.490755933 5.123989 6.233163e-05 +#> Lower Upper +#> T245_0 99.246061427 1.084640e+02 +#> k_T245 0.039631621 4.746194e-02 +#> k_phenol 0.218013878 7.525762e-01 +#> k_anisole 0.005370739 8.305299e-03 +#> f_T245_to_phenol 0.547559082 6.924813e-01 +#> f_phenol_to_anisole 0.000000000 1.000000e+00 +#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> T245_phenol T245_sink phenol_anisole phenol_sink +#> 6.227599e-01 3.772401e-01 1.000000e+00 1.005127e-10 +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784092 344.76329 +#> </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> + <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#> <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> T245_phenol T245_sink phenol_anisole phenol_sink +#> 6.227599e-01 3.772401e-01 1.000000e+00 1.005127e-10 +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784092 344.76329 +#> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'> # } +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a 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