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For time series, the function performs part of the residue -processing proposed in the FOCUS kinetics guidance for parent compounds -and metabolites. For two-dimensional residue series over time and depth, -it automates the proposal of Boesten et al (2015)." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- 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> - <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">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Set non-detects and unquantified values in residue series without replicates</h1> - - <div class="hidden name"><code>set_nd_nq.Rd</code></div> - </div> - - <div class="ref-description"> - <p>This function automates replacing unquantified values in residue time and -depth series. For time series, the function performs part of the residue -processing proposed in the FOCUS kinetics guidance for parent compounds -and metabolites. For two-dimensional residue series over time and depth, -it automates the proposal of Boesten et al (2015).</p> - </div> - - <pre class="usage"><span class='fu'>set_nd_nq</span>(<span class='no'>res_raw</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>set_nd_nq_focus</span>( - <span class='no'>res_raw</span>, - <span class='no'>lod</span>, - <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>set_first_sample_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>first_sample_nd_value</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>ignore_below_loq_after_first_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>res_raw</th> - <td><p>Character vector of a residue time series, or matrix of -residue values with rows representing depth profiles for a specific sampling -time, and columns representing time series of residues at the same depth. -Values below the limit of detection (lod) have to be coded as "nd", values -between the limit of detection and the limit of quantification, if any, have -to be coded as "nq". Samples not analysed have to be coded as "na". All -values that are not "na", "nd" or "nq" have to be coercible to numeric</p></td> - </tr> - <tr> - <th>lod</th> - <td><p>Limit of detection (numeric)</p></td> - </tr> - <tr> - <th>loq</th> - <td><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to -stop after the first non-detection is to be applied</p></td> - </tr> - <tr> - <th>time_zero_presence</th> - <td><p>Do we assume that residues occur at time zero? -This only affects samples from the first sampling time that have been -reported as "nd" (not detected).</p></td> - </tr> - <tr> - <th>set_first_sample_nd</th> - <td><p>Should the first sample be set to "first_sample_nd_value" -in case it is a non-detection?</p></td> - </tr> - <tr> - <th>first_sample_nd_value</th> - <td><p>Value to be used for the first sample if it is a non-detection</p></td> - </tr> - <tr> - <th>ignore_below_loq_after_first_nd</th> - <td><p>Should we ignore values below the LOQ after the first -non-detection that occurs after the quantified values?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> - <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2> - - -<ul> -<li><p><code>set_nd_nq_focus</code>: Set non-detects in residue time series according to FOCUS rules</p></li> -</ul> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. -J. and Pol, J. W. (2015). Leaching of plant protection products and their -transformation products; Proposals for improving the assessment of leaching -to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra -Wageningen UR (University & Research centre)</p> -<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, - 18 December 2014, p. 251</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># FOCUS (2014) p. 75/76 and 131/132</span> -<span class='no'>parent_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_3</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.06</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='no'>metabolite</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>0.03</span>, <span class='fl'>0.06</span>, <span class='fl'>0.10</span>, <span class='fl'>0.11</span>, <span class='fl'>0.10</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>, <span class='fl'>0.05</span>)</div><div class='output co'>#> [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</div><div class='input'><span class='co'>#</span> -<span class='co'># Boesten et al. (2015), p. 57/58</span> -<span class='no'>table_8</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>( - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>), - <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nq"</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>2</span>), - <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, - <span class='st'>"nq"</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>), - <span class='st'>"nd"</span>, <span class='st'>"nq"</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>), - <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>)), - <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>table_8</span>, <span class='fl'>0.5</span>, <span class='fl'>1.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [,1] [,2] [,3] [,4] [,5] [,6] -#> [1,] 10.00 10.00 0.25 0.25 NA NA -#> [2,] 10.00 10.00 1.00 1.00 0.25 NA -#> [3,] 10.00 10.00 10.00 1.00 0.25 NA -#> [4,] 1.00 10.00 1.00 0.25 NA NA -#> [5,] 0.25 1.00 1.00 0.25 NA NA -#> [6,] NA 0.25 0.25 NA NA NA -#> [7,] NA NA NA NA NA NA</div><div class='input'><span class='no'>table_10</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>( - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>), - <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>), - <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>), - <span class='st'>"nd"</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>), - <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>18</span>)), - <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>set_nd_nq</span>(<span class='no'>table_10</span>, <span class='fl'>0.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [,1] [,2] [,3] [,4] [,5] [,6] -#> [1,] 10.00 10.00 0.25 NA NA NA -#> [2,] 10.00 10.00 0.25 NA NA NA -#> [3,] 10.00 10.00 10.00 0.25 NA NA -#> [4,] 0.25 10.00 0.25 NA NA NA -#> [5,] NA 0.25 NA NA NA NA -#> [6,] NA NA NA NA NA NA -#> [7,] NA NA NA NA NA NA</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#functions">Functions</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - </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> 1.4.1.</p> -</div> - - </footer> - </div> - - - - - </body> -</html> - - |