aboutsummaryrefslogblamecommitdiff
path: root/docs/dev/reference/f_time_norm_focus.html
blob: b556df04d568841f72a680ccedcd3843dfcacaea (plain) (tree)
1
2
3
4
5
6
7
8
9
               

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                

                                                                               

                                                              
 
                                                    
                                                                                    









                                                                                                                               
                                                                                                                                        



                                                      
                                     


                                                          
                                                                                                                           



                               
                                            








                                                                                                 



                                                                                                                                                      




                                                                                                                             


                                                                                                   





                                                                                                                
                                                                                   
         



                                                                                              


                                       

                                                                  
                                             


      
                                       




                           
                                


                                                                                           
                                                                                                                                                                                   







                                                                                































































                                                                                                                                                                                                                                                                                                                

                                                                    
                                                           
 



                                                                  
                                                                         
                                                                          
                                                           

                                                                                                                                                           
                                                                         
                                                                          
                             






























                                                                                                                                                                                                                                                                                                                                          

                                                                 

                                                                                      


      

                                            


                     
                                                                                                             

      
                     



  
  
 
                
 
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus • 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="Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus"><meta property="og:description" content="Time step normalisation factors for aerobic soil degradation as described
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]>
<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">1.2.2</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" data-bs-toggle="dropdown" 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/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>
    </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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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">Benchmark timings for mkin</a>
    </li>
    <li>
      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</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/" class="external-link">
    <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>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="hidden name"><code>f_time_norm_focus.Rd</code></div>
    </div>

    <div class="ref-description">
    <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 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></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,
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 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>
  </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></p><p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>

      </footer></div>

  


  

  </body></html>

Contact - Imprint