From e2aa453b1d5535ceb2d0d7b042d2c3b68c6298d1 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 19 Dec 2020 12:24:43 +0100
Subject: Update docs
---
docs/dev/reference/dimethenamid_2018.html | 234 ++++++++++++++++++++++++++++++
docs/dev/reference/f_time_norm_focus.html | 34 +++--
docs/dev/reference/index.html | 6 +
3 files changed, 258 insertions(+), 16 deletions(-)
create mode 100644 docs/dev/reference/dimethenamid_2018.html
(limited to 'docs/dev/reference')
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
new file mode 100644
index 00000000..21dea623
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+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -0,0 +1,234 @@
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+published by EFSA. Kinetic evaluations shown for these datasets are intended
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/dimethenamid_2018.R'><code>R/dimethenamid_2018.R</code></a></small>
+ <div class="hidden name"><code>dimethenamid_2018.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>The datasets were extracted from the active substance evaluation dossier
+published by EFSA. Kinetic evaluations shown for these datasets are intended
+to illustrate and advance kinetic modelling. The fact that these data and
+some results are shown here does not imply a license to use them in the
+context of pesticide registrations, as the use of the data may be
+constrained by data protection regulations.</p>
+ </div>
+
+ <pre class="usage"><span class='va'>dimethenamid_2018</span></pre>
+
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <a href='mkindsg.html'>mkindsg</a> object grouping eight datasets with some meta information</p>
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
+Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
+Rev. 2 - November 2017
+<a href='http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211'>http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211</a></p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The R code used to create this data object is installed with this package
+in the 'dataset_generation' directory. In the code, page numbers are given for
+specific pieces of information in the comments.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>dimethenamid_2018</span><span class='op'>)</span>
+</div><div class='output co'>#> <mkindsg> holding 8 mkinds objects
+#> Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018
+#> Occurrence of observed compounds $observed_n:
+#> DMTAP M23 M27 M31 DMTA
+#> 4 7 7 7 4
+#> Time normalisation factors $f_time_norm:
+#> [1] 1.0000000 0.9706477 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922
+#> [8] 0.6733938
+#> Meta information $meta:
+#> study usda_soil_type study_moisture_ref_type
+#> Calke Unsworth 2014 Sandy loam pF2
+#> Borstel 1 Staudenmaier 2013 Sand pF1
+#> Borstel 2 Staudenmaier 2009 Sand pF1
+#> Elliot 1 Wendt 1997 Clay loam pF2.5
+#> Elliot 2 Wendt 1997 Clay loam pF2.5
+#> Flaach König 1996 Sandy clay loam pF1
+#> BBA 2.2 König 1995 Loamy sand pF1
+#> BBA 2.3 König 1995 Sandy loam pF1
+#> rel_moisture study_ref_moisture temperature
+#> Calke 1.00 NA 20
+#> Borstel 1 0.50 23.00 20
+#> Borstel 2 0.50 23.00 20
+#> Elliot 1 0.75 33.37 23
+#> Elliot 2 0.75 33.37 23
+#> Flaach 0.40 NA 20
+#> BBA 2.2 0.40 NA 20
+#> BBA 2.3 0.40 NA 20</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>
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+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
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diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html
index a95234a7..3421043d 100644
--- a/docs/dev/reference/f_time_norm_focus.html
+++ b/docs/dev/reference/f_time_norm_focus.html
@@ -122,7 +122,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -166,7 +166,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p>
<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'>"meta"</span>, <span class='st'>"focus"</span><span class='op'>)</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>,
@@ -213,7 +213,9 @@ for complete cases will be returned.</p></td>
<tr>
<th>study_moisture_ref_source</th>
<td><p>Source for the reference value
-used to calculate the study moisture</p></td>
+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>
@@ -237,22 +239,22 @@ Version 1.1, 18 December 2014
<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'>#> [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'>#> study usda_soil_type study_moisture_ref_type rel_moisture
-#> 1 Cohen 1991 Silt loam <NA> NA
-#> 2 Liu and Adelfinskaya 2011 Silt loam pF1 0.5
-#> 3 Liu and Adelfinskaya 2011 Loam pF1 0.5
-#> 4 Liu and Adelfinskaya 2011 Loam pF1 0.5
-#> 5 Liu and Adelfinskaya 2011 Loamy sand pF1 0.5
-#> temperature
-#> 1 25
-#> 2 20
-#> 3 20
-#> 4 20
-#> 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>
+</div><div class='output co'>#> study usda_soil_type study_moisture_ref_type
+#> Mississippi Cohen 1991 Silt loam <NA>
+#> Fayette Liu and Adelfinskaya 2011 Silt loam pF1
+#> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1
+#> Site E1 Liu and Adelfinskaya 2011 Loam pF1
+#> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1
+#> rel_moisture temperature
+#> Mississippi NA 25
+#> Fayette 0.5 20
+#> RefSol 03-G 0.5 20
+#> Site E1 0.5 20
+#> 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'>#> $time_norm was set to
-#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div><div class='output co'>#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre>
+#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index d2040184..e038ef5c 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -391,6 +391,12 @@ of an mmkin object</p></td>
<td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td>
</tr><tr>
+ <td>
+ <p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p>
+ </td>
+ <td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td>
+ </tr><tr>
+
<td>
<p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p>
</td>
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