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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:16:17 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:27:50 +0100
commitaed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 (patch)
tree7ca136834857c12449f50a1e086a589cc9b79e2e /docs/reference/soil_scenario_data_EFSA_2015.html
parent64f629efbe666bae56f48a309adf33d1eb09c358 (diff)
Reorganise data generation
- Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory
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<h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1>
@@ -116,81 +47,65 @@ concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the
scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
</div>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2015</span></span></code></pre></div>
+ </div>
-
- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
+ <div id="format">
+ <h2>Format</h2>
<p>A data frame with one row for each scenario. Row names are the scenario codes,
e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p>
- <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
-
+ </div>
+ <div id="source">
+ <h2>Source</h2>
<p>EFSA (European Food Safety Authority) (2015)
EFSA guidance document for predicting environmental concentrations
of active substances of plant protection products and transformation products of these
active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
- doi:10.2903/j.efsa.2015.4093</p>
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
- <span class='co'># This is the code that was used to define the data</span>
- <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(
- <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>),
- <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>),
- <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>),
- <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>),
- <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>),
- <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>),
- <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>),
- <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>),
- <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>),
- <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>),
- <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>)
- )
- <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>)
-}
-
-<span class='co'># And this is the resulting dataframe</span>
-<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#&gt; Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce
-#&gt; CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0
-#&gt; CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0
-#&gt; CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0
-#&gt; CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0
-#&gt; CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5
-#&gt; CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5
-#&gt; f_mod
-#&gt; CTN 2
-#&gt; CTC 2
-#&gt; CTS 2
-#&gt; CLN 4
-#&gt; CLC 4
-#&gt; CLS 4</div></pre>
+ <a href="https://doi.org/10.2903/j.efsa.2015.4093" class="external-link">doi:10.2903/j.efsa.2015.4093</a></p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_mod</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTN 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTC 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CTS 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLN 4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLC 4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> CLS 4</span>
+</code></pre></div>
+ </div>
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