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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/reference/f_time_norm_focus.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/reference/f_time_norm_focus.html')
-rw-r--r--docs/dev/reference/f_time_norm_focus.html330
1 files changed, 138 insertions, 192 deletions
diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html
index 852e00a0..b556df04 100644
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+in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -73,23 +18,21 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
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- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
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@@ -99,48 +42,50 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
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- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
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<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
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- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
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+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
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<div class="page-header">
<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>
+ <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="hidden name"><code>f_time_norm_focus.Rd</code></div>
</div>
@@ -149,137 +94,138 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
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
+ <div id="ref-usage">
+ <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 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 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 id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>An object containing information used for the calculations</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Currently not used</p></dd>
+
+
+<dt>moisture</dt>
+<dd><p>Numeric vector of moisture contents in \% w/w</p></dd>
+
+
+<dt>field_moisture</dt>
+<dd><p>Numeric vector of moisture contents at field capacity
+(pF2) in \% w/w</p></dd>
+
+
+<dt>temperature</dt>
+<dd><p>Numeric vector of temperatures in °C</p></dd>
+
+
+<dt>Q10</dt>
+<dd><p>The Q10 value used for temperature normalisation</p></dd>
+
+
+<dt>walker</dt>
+<dd><p>The Walker exponent used for moisture normalisation</p></dd>
+
+
+<dt>f_na</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>study_moisture_ref_source</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></td>
- </tr>
- </table>
+the focus soil moisture for the soil class is used</p></dd>
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+</dl></div>
+ <div id="references">
+ <h2>References</h2>
+ <p>FOCUS (2006) “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,
+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'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
-FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+<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&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+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'>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; $time_norm was set to
-#&gt; [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre>
+<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ </div>
+ <div id="see-also">
+ <h2>See also</h2>
+ <div class="dont-index"><p><a href="focus_soil_moisture.html">focus_soil_moisture</a></p></div>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.373956</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> study usda_soil_type study_moisture_ref_type</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Mississippi Cohen 1991 Silt loam &lt;NA&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> rel_moisture temperature</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Mississippi NA 25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fayette 0.5 20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> RefSol 03-G 0.5 20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Site E1 0.5 20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> $f_time_norm was (re)set to normalised values</span>
+</code></pre></div>
+ </div>
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