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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/test_data_from_UBA_2014.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/test_data_from_UBA_2014.html')
| -rw-r--r-- | docs/dev/reference/test_data_from_UBA_2014.html | 251 |
1 files changed, 251 insertions, 0 deletions
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class="page-header"> + <h1>Three experimental datasets from two water sediment systems and one soil</h1> + + <div class="hidden name"><code>test_data_from_UBA_2014.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014).</p> + </div> + + <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. + Each dataset has, among others, the following components</p><dl'> + <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> + <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> + +</dl> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> + <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> + <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span> + <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span> + <span class='co'># generally considered deprecated due to the frequent occurrence of such</span> + <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> + <span class='co'># model).</span> + <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_w_0 95.91998116 NA NA NA NA NA +#> k_parent_w 0.41145375 NA NA NA NA NA +#> k_parent_s 0.04663944 NA NA NA NA NA +#> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA +#> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA +#> sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.1090929 5 6 +#> parent_w 0.0817436 3 3 +#> parent_s 0.1619965 2 3</div><div class='input'> + <span class='co'># This is the evaluation used for the validation of software packages</span> + <span class='co'># in the expertise from 2014</span> + <span class='no'>m_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), + <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_0 76.55425584 0.859186419 89.1008681 1.113862e-26 74.755958720 +#> k_parent 0.12081956 0.004601919 26.2541703 1.077361e-16 0.111561576 +#> k_M1 0.84258629 0.806165149 1.0451783 1.545282e-01 0.113778910 +#> k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013823 +#> k_M3 0.01122919 0.007245870 1.5497364 6.885076e-02 0.002909418 +#> f_parent_to_M1 0.32240193 0.240785518 1.3389590 9.819221e-02 NA +#> f_parent_to_M2 0.16099854 0.033691991 4.7785404 6.531224e-05 NA +#> f_M1_to_M3 0.27921506 0.269425582 1.0363346 1.565282e-01 0.022977955 +#> f_M2_to_M3 0.55641331 0.595121774 0.9349571 1.807710e-01 0.008002320 +#> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 +#> Upper +#> parent_0 78.35255297 +#> k_parent 0.13084582 +#> k_M1 6.23974738 +#> k_M2 0.09843271 +#> k_M3 0.04334017 +#> f_parent_to_M1 NA +#> f_parent_to_M2 NA +#> f_M1_to_M3 0.86450905 +#> f_M2_to_M3 0.99489911 +#> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09649963 9 20 +#> parent 0.04721283 2 6 +#> M1 0.26551208 2 5 +#> M2 0.20327575 2 5 +#> M3 0.05196550 3 4</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 href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |