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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/HEAD/R/f_time_norm_focus.R" class="external-link"><code>R/f_time_norm_focus.R</code></a></small>
<div class="d-none name"><code>f_time_norm_focus.Rd</code></div>
</div>
<div class="ref-description section level2">
<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>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><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>
<span></span>
<span><span class="co"># S3 method for class 'numeric'</span></span>
<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span>
<span> <span class="va">object</span>,</span>
<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> field_moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> temperature <span class="op">=</span> <span class="va">object</span>,</span>
<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span>
<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span>
<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'mkindsg'</span></span>
<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span>
<span> <span class="va">object</span>,</span>
<span> study_moisture_ref_source <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</span>
<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span>
<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span>
<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>An object containing information used for the calculations</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Currently not used</p></dd>
<dt id="arg-moisture">moisture<a class="anchor" aria-label="anchor" href="#arg-moisture"></a></dt>
<dd><p>Numeric vector of moisture contents in \% w/w</p></dd>
<dt id="arg-field-moisture">field_moisture<a class="anchor" aria-label="anchor" href="#arg-field-moisture"></a></dt>
<dd><p>Numeric vector of moisture contents at field capacity
(pF2) in \% w/w</p></dd>
<dt id="arg-temperature">temperature<a class="anchor" aria-label="anchor" href="#arg-temperature"></a></dt>
<dd><p>Numeric vector of temperatures in °C</p></dd>
<dt id="arg-q-">Q10<a class="anchor" aria-label="anchor" href="#arg-q-"></a></dt>
<dd><p>The Q10 value used for temperature normalisation</p></dd>
<dt id="arg-walker">walker<a class="anchor" aria-label="anchor" href="#arg-walker"></a></dt>
<dd><p>The Walker exponent used for moisture normalisation</p></dd>
<dt id="arg-f-na">f_na<a class="anchor" aria-label="anchor" href="#arg-f-na"></a></dt>
<dd><p>The factor to use for NA values. If set to NA, only factors
for complete cases will be returned.</p></dd>
<dt id="arg-study-moisture-ref-source">study_moisture_ref_source<a class="anchor" aria-label="anchor" href="#arg-study-moisture-ref-source"></a></dt>
<dd><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></dd>
</dl></div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
<p>FOCUS (2006) “Guidance Document on Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
EU Registration” 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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
FOCUS (2014) “Generic guidance for Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
EU Registration” 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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><a href="focus_soil_moisture.html">focus_soil_moisture</a></p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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></span></span>
<span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span>
<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span>
<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span>
<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span>
<span class="r-in"><span><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span></span>
<span class="r-in"><span><span class="co"># temperature only normalisation as in the EU evaluation</span></span></span>
<span class="r-in"><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></span></span>
<span class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span>
</code></pre></div>
</div>
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