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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-12-19 12:24:43 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-12-19 12:24:43 +0100 |
| commit | e2aa453b1d5535ceb2d0d7b042d2c3b68c6298d1 (patch) | |
| tree | 0356a7012dd13c3083e9955f3e9769071523386f | |
| parent | e25f0194736a090914c10a9f374946c0b89adc5b (diff) | |
Update docs
| -rw-r--r-- | _pkgdown.yml | 1 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/dimethenamid_2018.html | 234 | ||||
| -rw-r--r-- | docs/dev/reference/f_time_norm_focus.html | 34 | ||||
| -rw-r--r-- | docs/dev/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/dev/sitemap.xml | 3 |
6 files changed, 263 insertions, 17 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml index 2ae14397..57f12fbf 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -54,6 +54,7 @@ reference: contents: - focus_soil_moisture - D24_2014 + - dimethenamid_2018 - FOCUS_2006_A - FOCUS_2006_SFO_ref_A_to_F - FOCUS_2006_FOMC_ref_A_to_F diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 4dd05c5b..b3124589 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-12-16T18:25Z +last_built: 2020-12-19T11:24Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html new file mode 100644 index 00000000..21dea623 --- /dev/null +++ b/docs/dev/reference/dimethenamid_2018.html @@ -0,0 +1,234 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018 • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018" /> +<meta property="og:description" content="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." /> + + +<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]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <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> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + 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 @@ -392,6 +392,12 @@ of an mmkin object</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> <td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 56a788dd..ecf68e50 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -67,6 +67,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc> </url> <url> |