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| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/f_time_norm_focus.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/f_time_norm_focus.html')
| -rw-r--r-- | docs/reference/f_time_norm_focus.html | 299 |
1 files changed, 111 insertions, 188 deletions
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -73,13 +18,12 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -88,8 +32,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,6 +42,9 @@ 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> <li> + <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -113,34 +59,27 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</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/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <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 +88,121 @@ 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> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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" 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>, + 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></code></pre></div> + </div> - <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="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> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence +the focus soil moisture for the soil class is used</p></dd> +</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” 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) “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” 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> +<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> - <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'>#> [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 -#> 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'>#> $time_norm was set to -#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span> +<span class="r-in"></span> +<span class="r-in"><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</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 class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span> +<span class="r-in"><span class="co"># temperature only normalisation as in the EU evaluation</span></span> +<span class="r-in"><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 class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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