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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /docs/reference/f_time_norm_focus.html
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
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+ <h1>Normalisation factors for aerobic soil degradation according to FOCUS guidance</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/f_time_norm_focus.R'><code>R/f_time_norm_focus.R</code></a></small>
+ <div class="hidden name"><code>f_time_norm_focus.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Time step normalisation factors for aerobic soil degradation as described
+in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for numeric</span>
+<span class='fu'>f_time_norm_focus</span><span class='op'>(</span>
+ <span class='va'>object</span>,
+ moisture <span class='op'>=</span> <span class='cn'>NA</span>,
+ field_moisture <span class='op'>=</span> <span class='cn'>NA</span>,
+ temperature <span class='op'>=</span> <span class='va'>object</span>,
+ Q10 <span class='op'>=</span> <span class='fl'>2.58</span>,
+ walker <span class='op'>=</span> <span class='fl'>0.7</span>,
+ f_na <span class='op'>=</span> <span class='cn'>NA</span>,
+ <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for mkindsg</span>
+<span class='fu'>f_time_norm_focus</span><span class='op'>(</span>
+ <span class='va'>object</span>,
+ study_moisture_ref_source <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"auto"</span>, <span class='st'>"meta"</span>, <span class='st'>"focus"</span><span class='op'>)</span>,
+ Q10 <span class='op'>=</span> <span class='fl'>2.58</span>,
+ walker <span class='op'>=</span> <span class='fl'>0.7</span>,
+ f_na <span class='op'>=</span> <span class='cn'>NA</span>,
+ <span class='va'>...</span>
+<span class='op'>)</span></pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>An object containing information used for the calculations</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Currently not used</p></td>
+ </tr>
+ <tr>
+ <th>moisture</th>
+ <td><p>Numeric vector of moisture contents in \% w/w</p></td>
+ </tr>
+ <tr>
+ <th>field_moisture</th>
+ <td><p>Numeric vector of moisture contents at field capacity
+(pF2) in \% w/w</p></td>
+ </tr>
+ <tr>
+ <th>temperature</th>
+ <td><p>Numeric vector of temperatures in °C</p></td>
+ </tr>
+ <tr>
+ <th>Q10</th>
+ <td><p>The Q10 value used for temperature normalisation</p></td>
+ </tr>
+ <tr>
+ <th>walker</th>
+ <td><p>The Walker exponent used for moisture normalisation</p></td>
+ </tr>
+ <tr>
+ <th>f_na</th>
+ <td><p>The factor to use for NA values. If set to NA, only factors
+for complete cases will be returned.</p></td>
+ </tr>
+ <tr>
+ <th>study_moisture_ref_source</th>
+ <td><p>Source for the reference value
+used to calculate the study moisture. If 'auto', preference is given
+to a reference moisture given in the meta information, otherwise
+the focus soil moisture for the soil class is used</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+Version 1.1, 18 December 2014
+<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><a href='focus_soil_moisture.html'>focus_soil_moisture</a></p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='fl'>25</span>, <span class='fl'>20</span>, <span class='fl'>25</span><span class='op'>)</span> <span class='co'># 1.37, compare FOCUS 2014 p. 184</span>
+</div><div class='output co'>#&gt; [1] 1.373956</div><div class='input'>
+<span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>meta</span>
+</div><div class='output co'>#&gt; study usda_soil_type study_moisture_ref_type
+#&gt; Mississippi Cohen 1991 Silt loam &lt;NA&gt;
+#&gt; Fayette Liu and Adelfinskaya 2011 Silt loam pF1
+#&gt; RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1
+#&gt; Site E1 Liu and Adelfinskaya 2011 Loam pF1
+#&gt; Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1
+#&gt; rel_moisture temperature
+#&gt; Mississippi NA 25
+#&gt; Fayette 0.5 20
+#&gt; RefSol 03-G 0.5 20
+#&gt; Site E1 0.5 20
+#&gt; Site I2 0.5 20</div><div class='input'><span class='co'># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span>
+<span class='co'># temperature only normalisation as in the EU evaluation</span>
+<span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>D24_2014</span>, study_moisture_ref_source <span class='op'>=</span> <span class='st'>"focus"</span>, f_na <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $time_norm was set to
+#&gt; [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre>
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