diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-16 18:02:18 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-16 18:02:18 +0200 |
| commit | d81550d0cccae824cc748de48e7fd50ea8d8033a (patch) | |
| tree | cb95252ff725b5dcd0237bb8f74fdac4a3e08d15 | |
| parent | 4bc95b3e4aae22e4052e0a4c905a9227c909e2cd (diff) | |
Make na.rm = FALSE the default for geomean()
This makes more sense and is in line with mean() from base R. Adapt
tests and update docs.
51 files changed, 723 insertions, 412 deletions
@@ -1,3 +1,9 @@ +commit 4bc95b3e4aae22e4052e0a4c905a9227c909e2cd +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2020-02-19 07:49:08 +0100 + + Check in last build log + commit 00e177fdf6929058fd26c3086ae159462ae0a456 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2019-10-23 16:18:24 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 9487deb..4d471dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.5.7 -Date: 2019-11-20 +Date: 2020-04-16 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) @@ -32,4 +32,4 @@ LazyLoad: yes LazyData: yes Encoding: UTF-8 URL: https://pkdown.jrwb.de/pfm -RoxygenNote: 6.1.1 +RoxygenNote: 7.0.2 diff --git a/R/geomean.R b/R/geomean.R index 626829b..04328c8 100644 --- a/R/geomean.R +++ b/R/geomean.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015,2020 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -19,8 +19,9 @@ #' #' Based on some posts in a thread on Stackoverflow #' \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -#' This function checks for negative values, removes NA values per default and -#' returns 0 if at least one element of the vector is 0. +#' This function returns NA if NA values are present and na.rm = FALSE +#' (default). If negative values are present, it gives an error message. +#' If at least one element of the vector is 0, it returns 0. #' #' @param x Vector of numbers #' @param na.rm Should NA values be omitted? @@ -31,8 +32,8 @@ #' geomean(c(1, 3, 9)) #' geomean(c(1, 3, NA, 9)) #' \dontrun{geomean(c(1, -3, 9)) # returns an error} -geomean = function(x, na.rm = TRUE){ - if (any(is.na(x)) & na.rm == FALSE) stop("Removal of NA values was not requested") +geomean = function(x, na.rm = FALSE) { + if (any(is.na(x)) & na.rm == FALSE) return(NA) if (any(x < 0, na.rm = na.rm)) stop("Only defined for positive numbers") exp(mean(log(x), na.rm = na.rm)) } diff --git a/docs/index.html b/docs/index.html index 23000f1..2e42649 100644 --- a/docs/index.html +++ b/docs/index.html @@ -75,7 +75,7 @@ <a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"pfm"</span>)</a></code></pre></div> <p>Alternatively you can install the package using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(devtools)</a> -<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</a></code></pre></div> </div> <div id="use" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 4eed02f..77045f1 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -8,11 +8,13 @@ <title>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios" /> +<meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios" /> <meta property="og:description" content="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear." /> <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> @@ -83,7 +86,6 @@ The text file is not included in the package as its licence is not clear." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,20 +107,18 @@ The text file is not included in the package as its licence is not clear." /> </div> <div class="ref-description"> - <p>The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear.</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing the scenario names in a character vector called 'names', the drift percentiles in a matrix called 'drift', interception percentages in a matrix called 'interception' and the runoff/drainage percentages for Step 2 calculations in a matrix called 'rd'.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -295,9 +295,7 @@ The text file is not included in the package as its licence is not clear.</p> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index ae6e38c..a365556 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -8,11 +8,13 @@ <title>Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa" /> +<meta property="og:title" content="Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa" /> <meta property="og:description" content="Actual and maximum moving window time average concentrations for FOMC kinetics" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,14 +106,15 @@ </div> <div class="ref-description"> - <p>Actual and maximum moving window time average concentrations for FOMC kinetics</p> - </div> - <pre class="usage"><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, - <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>))</pre> - + <pre class="usage"><span class='fu'>FOMC_actual_twa</span>( + <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, + <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, + <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</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> @@ -128,13 +131,12 @@ <td><p>The output times, and window sizes for time weighted average concentrations</p></td> </tr> </table> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <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='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> actual twa @@ -154,9 +156,7 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index b44c120..e371c1a 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -8,11 +8,13 @@ <title>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS" /> +<meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS" /> <meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> @@ -41,6 +43,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> + <!-- 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> @@ -84,7 +87,6 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -106,11 +108,9 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </div> <div class="ref-description"> - <p>The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> - </div> <pre class="usage"><span class='fu'>GUS</span>(<span class='no'>...</span>) @@ -119,14 +119,20 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> <span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>) <span class='co'># S3 method for chent</span> -<span class='fu'>GUS</span>(<span class='no'>chent</span>, <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>) +<span class='fu'>GUS</span>( + <span class='no'>chent</span>, + <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, + <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, + <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, + <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, + <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, + <span class='no'>...</span> +) <span class='co'># S3 method for GUS_result</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</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> @@ -198,29 +204,25 @@ be Koc values at a concentration of 1 mg/L in the water phase.</p></td> <td><p>The number of digits used in the print method</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with the DT50 and Koc used as well as the resulting score of class GUS_result</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. <em>Environmental toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> - </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="#references">References</a></li> - </ul> + </ul> <h2>Author</h2> <p>Johannes Ranke</p> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 81575f3..3e405a5 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -8,11 +8,13 @@ <title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil" /> +<meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil" /> <meta property="og:description" content="This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. If an interval is given, an attempt is made at calculating a long term maximum concentration using @@ -43,6 +45,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> + <!-- 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> @@ -86,7 +89,6 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -108,24 +110,38 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> </div> <div class="ref-description"> - <p>This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> - </div> - <pre class="usage"><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, - <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, - <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>, - <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>t_act</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <pre class="usage"><span class='fu'>PEC_soil</span>( + <span class='no'>rate</span>, + <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, + <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, + <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, + <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, + <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, + <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>, + <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>, + <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, + <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='kw'>t_act</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2017"</span>, <span class='st'>"EFSA_2015"</span>), - <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span> <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - + <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span> <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, + <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</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> @@ -245,11 +261,10 @@ soil concentrations? Based on equation (7) given in the PPR panel opinion p. 13).</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The predicted concentration in soil</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>This assumes that the complete load to soil during the time specified by @@ -258,7 +273,6 @@ opinion cited below (EFSA PPR panel 2012), only temperature correction using the Arrhenius equation is performed.</p> <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>While time weighted average (TWA) concentrations given in the examples @@ -275,7 +289,6 @@ from 2017 (p. 92).</p> e.g. in the EFSA scenarios, the DT50 for groundwater modelling (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>EFSA Panel on Plant Protection Products and their Residues (2012) @@ -293,7 +306,6 @@ from 2017 (p. 92).</p> protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 doi:10.2903/j.efsa.2015.4093</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> scenario @@ -334,15 +346,10 @@ from 2017 (p. 92).</p> <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="#details">Details</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index f641773..bdcf5af 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -8,11 +8,13 @@ <title>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK" /> +<meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK" /> <meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website" /> <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> @@ -83,7 +86,6 @@ published on the CRC website" /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,16 +107,20 @@ published on the CRC website" /> </div> <div class="ref-description"> - <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, - <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> - + <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>( + <span class='no'>rate</span>, + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='no'>Koc</span>, + <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</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> @@ -148,11 +154,10 @@ published on the CRC website</p> <td><p>A named numeric vector containing the model parameters</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The predicted concentration in surface water in µg/L</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance @@ -162,7 +167,6 @@ published on the CRC website</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> @@ -171,11 +175,8 @@ published on the CRC website</p> <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="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 14ccf79..302ab0d 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -8,11 +8,13 @@ <title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift" /> +<meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift" /> <meta property="og:description" content="This is a basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing with input via spray drift." /> @@ -41,6 +43,7 @@ with input via spray drift." /> + <!-- 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> @@ -84,7 +87,6 @@ with input via spray drift." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -106,18 +108,23 @@ with input via spray drift." /> </div> <div class="ref-description"> - <p>This is a basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing with input via spray drift.</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_drift</span>(<span class='no'>rate</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, - <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, - <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre> - + <pre class="usage"><span class='fu'>PEC_sw_drift</span>( + <span class='no'>rate</span>, + <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, + <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, + <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, + <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), + <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, + <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</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> @@ -159,11 +166,10 @@ with input via spray drift.</p> <td><p>Requested units for the calculated PEC. Only µg/L currently supported</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The predicted concentration in surface water</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m @@ -173,9 +179,7 @@ with input via spray drift.</p> <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="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 1c2deac..5bd1d80 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -8,11 +8,13 @@ <title>Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage" /> +<meta property="og:title" content="Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage" /> <meta property="og:description" content="This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Drainage". Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the @@ -45,6 +47,7 @@ details, see the discussion of the function arguments below." /> + <!-- 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> @@ -88,7 +91,6 @@ details, see the discussion of the function arguments below." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -110,7 +112,6 @@ details, see the discussion of the function arguments below." /> </div> <div class="ref-description"> - <p>This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Drainage". Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the @@ -118,14 +119,20 @@ calculations, between compounds with low mobility (group 1) and compounds with modest to high mobility (groups 2, 3 and 4). In this implementation, the group is derived only from the Koc, if not given explicitly. For details, see the discussion of the function arguments below.</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_drainage</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>mobility</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"low"</span>, <span class='st'>"high"</span>), <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>t_drainage</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>V_drainage</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>spring</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>autumn</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre> - + <pre class="usage"><span class='fu'>PEC_sw_exposit_drainage</span>( + <span class='no'>rate</span>, + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>mobility</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"low"</span>, <span class='st'>"high"</span>), + <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, + <span class='kw'>t_drainage</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, + <span class='kw'>V_drainage</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>spring</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>autumn</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</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> @@ -168,12 +175,11 @@ autumn/winter/early spring.</p></td> <td><p>The dilution factor</p></td> </tr> </table> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Excel 3.02 spreadsheet available from <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list containing the following components</p><dl class='dl-horizontal'> @@ -184,11 +190,9 @@ autumn/winter/early spring.</p></td> </dl> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_drainage</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_drainage_total @@ -208,13 +212,9 @@ autumn/winter/early spring.</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 30ef975..81549e0 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -8,11 +8,13 @@ <title>Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff" /> +<meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff" /> <meta property="og:description" content="This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Runoff"." /> <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> @@ -83,7 +86,6 @@ in the worksheet "Konzept Runoff"." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,16 +107,22 @@ in the worksheet "Konzept Runoff"." /> </div> <div class="ref-description"> - <p>This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Runoff".</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>, - <span class='st'>"3.01a2"</span>, <span class='st'>"2.0"</span>), <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre> - + <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>( + <span class='no'>rate</span>, + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='no'>Koc</span>, + <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, + <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>, <span class='st'>"3.01a2"</span>, <span class='st'>"2.0"</span>), + <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, + <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</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> @@ -159,12 +167,11 @@ and the bound fraction.</p></td> <td><p>The dilution factor</p></td> </tr> </table> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Excel 3.02 spreadsheet available from <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list containing the following components</p><dl class='dl-horizontal'> @@ -175,11 +182,9 @@ and the bound fraction.</p></td> </dl> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_runoff @@ -226,13 +231,9 @@ and the bound fraction.</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 1647b19..8242f6a 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -8,11 +8,13 @@ <title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" /> +<meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" /> <meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a @@ -45,6 +47,7 @@ to be used with the FOCUS calculator." /> + <!-- 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> @@ -88,7 +91,6 @@ to be used with the FOCUS calculator." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -110,7 +112,6 @@ to be used with the FOCUS calculator." /> </div> <div class="ref-description"> - <p>This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a @@ -118,16 +119,28 @@ single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator.</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, - <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>), - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, - <span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - + <pre class="usage"><span class='fu'>PEC_sw_focus</span>( + <span class='no'>parent</span>, + <span class='no'>rate</span>, + <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, + <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, + <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, + <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), + <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>), + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, <span class='st'>"average crop cover"</span>, + <span class='st'>"full canopy"</span>), + <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, + <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>append</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> @@ -214,7 +227,7 @@ should be written</p></td> <td><p>Should the input text file be appended?</p></td> </tr> </table> - + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The formulas for input to the waterbody via runoff/drainage of the @@ -224,7 +237,6 @@ should be written</p></td> multiplying the application rate with the molar weight correction and the formation fraction in water/sediment systems.</p> <p>Step 2 is not implemented.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). @@ -233,7 +245,6 @@ should be written</p></td> <p>Website of the Steps 1 and 2 calculator at the Joint Research Center of the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Parent only</span> @@ -337,11 +348,8 @@ should be written</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index fe65d96..458eeb7 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -9,11 +9,13 @@ <title>Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -33,15 +35,16 @@ water concentrations — PEC_sw_sed • pfm</title> + <meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed" /> - <meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator" /> <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> @@ -85,7 +88,6 @@ PEC calculator" /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -108,16 +110,20 @@ water concentrations</h1> </div> <div class="ref-description"> - <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator</p> - </div> - <pre class="usage"><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, - <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, - <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre> - + <pre class="usage"><span class='fu'>PEC_sw_sed</span>( + <span class='no'>PEC_sw</span>, + <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, + <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, + <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, + <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, + <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</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> @@ -152,11 +158,10 @@ g/cm3)</p></td> <td><p>The units of the estimated sediment PEC value</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The predicted concentration in sediment</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> 1 m @@ -166,9 +171,7 @@ g/cm3)</p></td> <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="#examples">Examples</a></li> </ul> diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index 1f172c6..b5fa5da 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -8,11 +8,13 @@ <title>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa" /> +<meta property="og:title" content="Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa" /> <meta property="og:description" content="Actual and maximum moving window time average concentrations for SFO kinetics" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,14 +106,11 @@ </div> <div class="ref-description"> - <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> - </div> - <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, - <span class='fl'>50</span>, <span class='fl'>100</span>))</pre> - + <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</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> @@ -124,13 +123,12 @@ <td><p>The output times, and window sizes for time weighted average concentrations</p></td> </tr> </table> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <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='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#> actual twa @@ -150,9 +148,7 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 8939850..cedb023 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -8,11 +8,13 @@ <title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" /> +<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" /> <meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> <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> @@ -83,7 +86,6 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,23 +107,33 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </div> <div class="ref-description"> - <p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> - </div> - <pre class="usage"><span class='no'>TOXSWA_cwa</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>An <code>R6Class</code> generator object.</p> - - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> + <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> <dl class='dl-horizontal'> + <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value + in µg/L. If <code>total = TRUE</code>, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + <code>events</code> field of the object.</p></dd> + <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above. + Again, if <code>total = TRUE</code>, the total concentration including the amount + adsorbed to suspended matter will be used.</p></dd> + +</dl> + + <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> + + <p><div class="r6-fields"></p><dl class='dl-horizontal'> <dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd> <dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd> @@ -136,24 +148,62 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.</p></dd> -</dl> - +</dl><p></div></p> <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +<h3>Public methods</h3> -<dl class='dl-horizontal'> - <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value - in µg/L. If <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - <code>events</code> field of the object.</p></dd> - <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above. - Again, if <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used.</p></dd> +<ul> +<li><p><a href='#method-new'><code>TOXSWA_cwa$new()</code></a></p></li> +<li><p><a href='#method-moving_windows'><code>TOXSWA_cwa$moving_windows()</code></a></p></li> +<li><p><a href='#method-get_events'><code>TOXSWA_cwa$get_events()</code></a></p></li> +<li><p><a href='#method-print'><code>TOXSWA_cwa$print()</code></a></p></li> +<li><p><a href='#method-clone'><code>TOXSWA_cwa$clone()</code></a></p></li> +</ul> +<p><hr> +<a id="method-new"></a></p><h3>Method <code>new()</code></h3> + +<h3>Usage</h3> +<p><div class="r"></p><pre>TOXSWA_cwa$new( + filename, + basedir, + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE +)</pre><p></div></p> + +<p><hr> +<a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> + +<h3>Usage</h3> +<p><div class="r"></p><pre>TOXSWA_cwa$moving_windows(windows, total = FALSE)</pre><p></div></p> + +<p><hr> +<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> + +<h3>Usage</h3> +<p><div class="r"></p><pre>TOXSWA_cwa$get_events(thresholds, total = FALSE)</pre><p></div></p> + +<p><hr> +<a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> + +<h3>Usage</h3> +<p><div class="r"></p><pre>TOXSWA_cwa$print()</pre><p></div></p> + +<p><hr> +<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> +<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> +<p><div class="r"></p><pre>TOXSWA_cwa$clone(deep = FALSE)</pre><p></div></p> + +<h3>Arguments</h3> +<p><div class="arguments"></p><dl class='dl-horizontal'> +<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> + +</dl><p></div></p> -</dl> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, @@ -192,13 +242,10 @@ for the requested moving window sizes in days.</p></dd> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - - <li><a href="#fields">Fields</a></li> - <li><a href="#methods">Methods</a></li> - + <li><a href="#public-fields">Public fields</a></li> + <li><a href="#methods">Methods</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 324f2fe..70fd16d 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -8,11 +8,13 @@ <title>Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw" /> +<meta property="og:title" content="Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw" /> <meta property="og:description" content="Create a chemical compound object for FOCUS Step 1 calculations" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,15 +106,22 @@ </div> <div class="ref-description"> - <p>Create a chemical compound object for FOCUS Step 1 calculations</p> - </div> - <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> - + <pre class="usage"><span class='fu'>chent_focus_sw</span>( + <span class='no'>name</span>, + <span class='no'>Koc</span>, + <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, + <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</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> @@ -159,20 +168,18 @@ in L/kg.</p></td> systems</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with the substance specific properties</p> - </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> - </ul> + </ul> </div> </div> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 99e407c..39071ee 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -8,11 +8,13 @@ <title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint" /> +<meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint" /> <meta property="og:description" content="R6 class objects of class chent represent chemical entities and can hold a list of information loaded from a chemical yaml file in their chyaml field. Such information is extracted and optionally aggregated by @@ -42,6 +44,7 @@ this function." /> + <!-- 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> @@ -85,7 +88,6 @@ this function." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -107,32 +109,46 @@ this function." /> </div> <div class="ref-description"> - <p>R6 class objects of class chent represent chemical entities and can hold a list of information loaded from a chemical yaml file in their chyaml field. Such information is extracted and optionally aggregated by this function.</p> - </div> - <pre class="usage"><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, - <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), - <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>) - -<span class='fu'>soil_DT50</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + <pre class="usage"><span class='fu'>endpoint</span>( + <span class='no'>chent</span>, + <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, + <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), + <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, <span class='st'>"anaerobic"</span>), + <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), + <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span> +) + +<span class='fu'>soil_DT50</span>( + <span class='no'>chent</span>, + <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, + <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, + <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, + <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> +) + +<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> - <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>), - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - +<span class='fu'>soil_sorption</span>( + <span class='no'>chent</span>, + <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), + <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), + <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>), + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</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> @@ -185,7 +201,7 @@ about precision?</p></td> <td><p>A named vector of aggregator functions to be used</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The result from applying the aggregator function to @@ -193,25 +209,21 @@ about precision?</p></td> given number of significant digits, or, if raw = TRUE, the values as a character value, retaining any implicit information on precision that may be present.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. For the Freundlich exponent, the capital letter <code>N</code> is used in order to facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.</p> - </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="#details">Details</a></li> - </ul> + </ul> </div> </div> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 469e12f..34befc3 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -8,11 +8,13 @@ <title>Calculate the geometric mean — geomean • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,16 +34,18 @@ -<meta property="og:title" content="Calculate the geometric mean — geomean" /> +<meta property="og:title" content="Calculate the geometric mean — geomean" /> <meta property="og:description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0." /> +This function returns NA if NA values are present and na.rm = FALSE +(default). If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0." /> <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> @@ -85,7 +89,6 @@ returns 0 if at least one element of the vector is 0." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -107,16 +110,15 @@ returns 0 if at least one element of the vector is 0." /> </div> <div class="ref-description"> - <p>Based on some posts in a thread on Stackoverflow <a href='http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0.</p> - +This function returns NA if NA values are present and na.rm = FALSE +(default). If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0.</p> </div> - <pre class="usage"><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - + <pre class="usage"><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</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> @@ -129,22 +131,19 @@ returns 0 if at least one element of the vector is 0.</p> <td><p>Should NA values be omitted?</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The geometric mean</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span></div></pre> + <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] NA</div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span></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="#examples">Examples</a></li> </ul> diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 56d60c0..cf58a58 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -8,11 +8,13 @@ <title>Create a time series of decline data — one_box • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Create a time series of decline data — one_box" /> +<meta property="og:title" content="Create a time series of decline data — one_box" /> <meta property="og:description" content="Create a time series of decline data" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,9 +106,7 @@ </div> <div class="ref-description"> - <p>Create a time series of decline data</p> - </div> <pre class="usage"><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) @@ -115,13 +115,11 @@ <span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) <span class='co'># S3 method for character</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) +<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) <span class='co'># S3 method for mkinfit</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre> - +<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</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> @@ -158,11 +156,10 @@ all observed variables.</p></td> <td><p>A named numeric vector containing the model parameters</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://rdrr.io/r/stats/ts.html'>ts</a></code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span> @@ -181,9 +178,7 @@ all observed variables.</p></td> <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="#examples">Examples</a></li> </ul> diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 7e4eab1..d2e62f6 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -8,11 +8,13 @@ <title>Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" /> +<meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" /> <meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,15 +106,18 @@ </div> <div class="ref-description"> - <p>Calculate a time course of relative concentrations based on an mkinmod model</p> - </div> - <pre class="usage"><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> - <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, - <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>))</pre> - + <pre class="usage"><span class='fu'>pfm_degradation</span>( + <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, + <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, + <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), + <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</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> @@ -143,7 +148,7 @@ is calculated (SFO model).</p></td> <td><p>The output times</p></td> </tr> </table> - + <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/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent @@ -158,7 +163,6 @@ is calculated (SFO model).</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 8ca5b8e..1262c71 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -8,11 +8,13 @@ <title>Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa" /> +<meta property="og:title" content="Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa" /> <meta property="og:description" content="Plot TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body." /> <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> @@ -83,7 +86,6 @@ segment of a TOXSWA surface water body." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,18 +107,24 @@ segment of a TOXSWA surface water body." /> </div> <div class="ref-description"> - <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body.</p> - </div> <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, - <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre> - +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, + <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, + <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, + <span class='no'>...</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> @@ -162,7 +170,7 @@ to suspended matter?</p></td> <td><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></td> </tr> </table> - + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>, @@ -178,7 +186,6 @@ to suspended matter?</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png Binary files differindex fc8116b..ad93165 100644 --- a/docs/reference/plot.one_box-3.png +++ b/docs/reference/plot.one_box-3.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index d048d22..75b8fe9 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -8,11 +8,13 @@ <title>Plot time series of decline data — plot.one_box • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Plot time series of decline data — plot.one_box" /> +<meta property="og:title" content="Plot time series of decline data — plot.one_box" /> <meta property="og:description" content="Plot time series of decline data" /> <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> @@ -82,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,16 +106,21 @@ </div> <div class="ref-description"> - <p>Plot time series of decline data</p> - </div> <pre class="usage"><span class='co'># S3 method for one_box</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre> - +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</span>)), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, + <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], + <span class='no'>...</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> @@ -152,11 +159,10 @@ be shown if max_twa is not NULL.</p></td> <td><p>Further arguments passed to methods</p></td> </tr> </table> - + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</a></code></p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) @@ -170,9 +176,7 @@ be shown if max_twa is not NULL.</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index df84634..9c5c2a0 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -8,11 +8,13 @@ <title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" /> +<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" /> <meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour @@ -44,6 +46,7 @@ renamed to ConLiqWatLay in the out file." /> + <!-- 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> @@ -87,7 +90,6 @@ renamed to ConLiqWatLay in the out file." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -109,20 +111,25 @@ renamed to ConLiqWatLay in the out file." /> </div> <div class="ref-description"> - <p>Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</p> - </div> - <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> - + <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>( + <span class='no'>filename</span>, + <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, + <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, + <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, + <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</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> @@ -167,12 +174,11 @@ maximum time weighted average concentrations and areas under the curve.</p></td> generating event statistics.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>An instance of an R6 object of class <code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>, @@ -184,9 +190,7 @@ generating event statistics.</p></td> <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="#examples">Examples</a></li> </ul> diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex fc8116b..ad93165 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index c6756a9..7720afc 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -8,11 +8,13 @@ <title>Create decline time series for multiple applications — sawtooth • pfm</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Create decline time series for multiple applications — sawtooth" /> +<meta property="og:title" content="Create decline time series for multiple applications — sawtooth" /> <meta property="og:description" content="If the application pattern is specified in applications, n and i are disregarded." /> <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> @@ -83,7 +86,6 @@ n and i are disregarded." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,15 +107,17 @@ n and i are disregarded." /> </div> <div class="ref-description"> - <p>If the application pattern is specified in <code>applications</code>, <code>n</code> and <code>i</code> are disregarded.</p> - </div> - <pre class="usage"><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, - (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre> - + <pre class="usage"><span class='fu'>sawtooth</span>( + <span class='no'>x</span>, + <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, + <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</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> @@ -136,7 +140,7 @@ is ignored</p></td> the corresponding amounts applied in the second column.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) @@ -162,7 +166,6 @@ the corresponding amounts applied in the second column.</p></td> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 9ec17ea..702b3e3 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -119,8 +119,14 @@ it automates the proposal of Boesten et al (2015).</p> <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> +<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"> diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd index f58dea7..0547d61 100644 --- a/man/FOCUS_Step_12_scenarios.Rd +++ b/man/FOCUS_Step_12_scenarios.Rd @@ -19,14 +19,14 @@ The text file is not included in the package as its licence is not clear. scenario_path <- "inst/extdata/FOCUS_Step_12_scenarios.txt" scenarios <- readLines(scenario_path)[9:38] FOCUS_Step_12_scenarios <- list() - sce <- read.table(text = scenarios, sep = "\\t", header = TRUE, check.names = FALSE, + sce <- read.table(text = scenarios, sep = "\t", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) FOCUS_Step_12_scenarios$names = sce$Crop rownames(sce) <- sce$Crop FOCUS_Step_12_scenarios$drift = sce[, 3:11] FOCUS_Step_12_scenarios$interception = sce[, 12:15] sce_2 <- readLines(scenario_path)[41:46] - rd <- read.table(text = sce_2, sep = "\\t")[1:2] + rd <- read.table(text = sce_2, sep = "\t")[1:2] rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) dimnames(rd_mat) = list(Time = c("Oct-Feb", "Mar-May", "Jun-Sep"), Region = c("North", "South")) diff --git a/man/FOMC_actual_twa.Rd b/man/FOMC_actual_twa.Rd index 2c40048..a0c7284 100644 --- a/man/FOMC_actual_twa.Rd +++ b/man/FOMC_actual_twa.Rd @@ -9,8 +9,11 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation 18 December 2014, p. 251 } \usage{ -FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, - 14, 21, 28, 42, 50, 100)) +FOMC_actual_twa( + alpha = 1.0001, + beta = 10, + times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) +) } \arguments{ \item{alpha}{Parameter of the FOMC model} @@ -11,10 +11,16 @@ GUS(...) \method{GUS}{numeric}(DT50, Koc, ...) -\method{GUS}{chent}(chent, degradation_value = "DT50ref", - lab_field = "laboratory", redox = "aerobic", - sorption_value = "Kfoc", degradation_aggregator = geomean, - sorption_aggregator = geomean, ...) +\method{GUS}{chent}( + chent, + degradation_value = "DT50ref", + lab_field = "laboratory", + redox = "aerobic", + sorption_value = "Kfoc", + degradation_aggregator = geomean, + sorption_aggregator = geomean, + ... +) \method{print}{GUS_result}(x, ..., digits = 1) } diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index a9e6c49..a198f24 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -4,14 +4,30 @@ \alias{PEC_soil} \title{Calculate predicted environmental concentrations in soil} \usage{ -PEC_soil(rate, rate_units = "g/ha", interception = 0, - mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", - interval = NA, n_periods = Inf, tillage_depth = 20, - leaching_depth = tillage_depth, crop = "annual", - cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, - Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, +PEC_soil( + rate, + rate_units = "g/ha", + interception = 0, + mixing_depth = 5, + PEC_units = "mg/kg", + PEC_pw_units = "mg/L", + interval = NA, + n_periods = Inf, + tillage_depth = 20, + leaching_depth = tillage_depth, + crop = "annual", + cultivation = FALSE, + chent = NA, + DT50 = NA, + FOMC = NA, + Koc = NA, + Kom = Koc/1.724, + t_avg = 0, + t_act = NULL, scenarios = c("default", "EFSA_2017", "EFSA_2015"), - leaching = scenarios == "EFSA_2017", porewater = FALSE) + leaching = scenarios == "EFSA_2017", + porewater = FALSE +) } \arguments{ \item{rate}{Application rate in units specified below} diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd index c9f8ed4..98aa868 100644 --- a/man/PEC_sw_drainage_UK.Rd +++ b/man/PEC_sw_drainage_UK.Rd @@ -4,9 +4,15 @@ \alias{PEC_sw_drainage_UK} \title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} \usage{ -PEC_sw_drainage_UK(rate, interception = 0, Koc, - latest_application = NULL, soil_DT50 = NULL, model = NULL, - model_parms = NULL) +PEC_sw_drainage_UK( + rate, + interception = 0, + Koc, + latest_application = NULL, + soil_DT50 = NULL, + model = NULL, + model_parms = NULL +) } \arguments{ \item{rate}{Application rate in g/ha} diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd index dfc3f39..cde3c78 100644 --- a/man/PEC_sw_drift.Rd +++ b/man/PEC_sw_drift.Rd @@ -4,10 +4,17 @@ \alias{PEC_sw_drift} \title{Calculate predicted environmental concentrations in surface water due to drift} \usage{ -PEC_sw_drift(rate, applications = 1, water_depth = 30, - drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", - distances = c(1, 5, 10, 20), rate_units = "g/ha", - PEC_units = "µg/L") +PEC_sw_drift( + rate, + applications = 1, + water_depth = 30, + drift_percentages = NULL, + drift_data = "JKI", + crop = "Ackerbau", + distances = c(1, 5, 10, 20), + rate_units = "g/ha", + PEC_units = "µg/L" +) } \arguments{ \item{rate}{Application rate in units specified below} diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd index 237d8cf..5a543c8 100644 --- a/man/PEC_sw_exposit_drainage.Rd +++ b/man/PEC_sw_exposit_drainage.Rd @@ -8,10 +8,17 @@ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} } \usage{ -PEC_sw_exposit_drainage(rate, interception = 0, Koc = NA, - mobility = c(NA, "low", "high"), DT50 = Inf, t_drainage = 3, - V_ditch = 30, V_drainage = c(spring = 10, autumn = 100), - dilution = 2) +PEC_sw_exposit_drainage( + rate, + interception = 0, + Koc = NA, + mobility = c(NA, "low", "high"), + DT50 = Inf, + t_drainage = 3, + V_ditch = 30, + V_drainage = c(spring = 10, autumn = 100), + dilution = 2 +) } \arguments{ \item{rate}{The application rate in g/ha} diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd index c73270b..a415a63 100644 --- a/man/PEC_sw_exposit_runoff.Rd +++ b/man/PEC_sw_exposit_runoff.Rd @@ -8,9 +8,17 @@ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} } \usage{ -PEC_sw_exposit_runoff(rate, interception = 0, Koc, DT50 = Inf, - t_runoff = 3, exposit_reduction_version = c("3.02", "3.01a", - "3.01a2", "2.0"), V_ditch = 30, V_event = 100, dilution = 2) +PEC_sw_exposit_runoff( + rate, + interception = 0, + Koc, + DT50 = Inf, + t_runoff = 3, + exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"), + V_ditch = 30, + V_event = 100, + dilution = 2 +) } \arguments{ \item{rate}{The application rate in g/ha} diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index 836ed86..3ad1ad0 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -4,12 +4,25 @@ \alias{PEC_sw_focus} \title{Calculate PEC surface water at FOCUS Step 1} \usage{ -PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL, - f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, - region = c("n", "s"), season = c(NA, "of", "mm", "js"), - interception = c("no interception", "minimal crop cover", - "average crop cover", "full canopy"), met_form_water = TRUE, - txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE) +PEC_sw_focus( + parent, + rate, + n = 1, + i = NA, + comment = "", + met = NULL, + f_drift = NA, + f_rd = 0.1, + scenario = FOCUS_Step_12_scenarios$names, + region = c("n", "s"), + season = c(NA, "of", "mm", "js"), + interception = c("no interception", "minimal crop cover", "average crop cover", + "full canopy"), + met_form_water = TRUE, + txt_file = "pesticide.txt", + overwrite = FALSE, + append = TRUE +) } \arguments{ \item{parent}{A list containing substance specific parameters, e.g. diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd index 1feb146..bc82ee3 100644 --- a/man/PEC_sw_sed.Rd +++ b/man/PEC_sw_sed.Rd @@ -5,9 +5,15 @@ \title{Calculate predicted environmental concentrations in sediment from surface water concentrations} \usage{ -PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, water_depth = 30, sediment_density = 1.3, - PEC_sed_units = c("µg/kg", "mg/kg")) +PEC_sw_sed( + PEC_sw, + percentage = 100, + method = "percentage", + sediment_depth = 5, + water_depth = 30, + sediment_density = 1.3, + PEC_sed_units = c("µg/kg", "mg/kg") +) } \arguments{ \item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd index 30039f2..bdf4c4d 100644 --- a/man/SFO_actual_twa.Rd +++ b/man/SFO_actual_twa.Rd @@ -9,8 +9,7 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation 18 December 2014, p. 251 } \usage{ -SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, - 50, 100)) +SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) } \arguments{ \item{DT50}{The half-life.} diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index f073180..eb3fe38 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -5,31 +5,10 @@ \alias{TOXSWA_cwa} \title{R6 class for holding TOXSWA water concentration data and associated statistics} \format{An \code{\link{R6Class}} generator object.} -\usage{ -TOXSWA_cwa -} \description{ An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. } -\section{Fields}{ - -\describe{ -\item{\code{filename}}{Length one character vector.} - -\item{\code{basedir}}{Length one character vector.} - -\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} - -\item{\code{cwas}}{Dataframe holding the concentrations.} - -\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} - -\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) -and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -for the requested moving window sizes in days.} -}} - \section{Methods}{ \describe{ @@ -57,3 +36,88 @@ H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) } \keyword{data} +\section{Public fields}{ +\if{html}{\out{<div class="r6-fields">}} +\describe{ +\item{\code{filename}}{Length one character vector.} + +\item{\code{basedir}}{Length one character vector.} + +\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} + +\item{\code{cwas}}{Dataframe holding the concentrations.} + +\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} + +\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.} +} +\if{html}{\out{</div>}} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-new}{\code{TOXSWA_cwa$new()}} +\item \href{#method-moving_windows}{\code{TOXSWA_cwa$moving_windows()}} +\item \href{#method-get_events}{\code{TOXSWA_cwa$get_events()}} +\item \href{#method-print}{\code{TOXSWA_cwa$print()}} +\item \href{#method-clone}{\code{TOXSWA_cwa$clone()}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-new"></a>}} +\subsection{Method \code{new()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new( + filename, + basedir, + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE +)}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-moving_windows"></a>}} +\subsection{Method \code{moving_windows()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-get_events"></a>}} +\subsection{Method \code{get_events()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-print"></a>}} +\subsection{Method \code{print()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-clone"></a>}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$clone(deep = FALSE)}\if{html}{\out{</div>}} +} + +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{</div>}} +} +} +} diff --git a/man/chent_focus_sw.Rd b/man/chent_focus_sw.Rd index 9830ade..5f595d8 100644 --- a/man/chent_focus_sw.Rd +++ b/man/chent_focus_sw.Rd @@ -4,9 +4,18 @@ \alias{chent_focus_sw} \title{Create a chemical compound object for FOCUS Step 1 calculations} \usage{ -chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, - DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, - max_soil = 1, max_ws = 1) +chent_focus_sw( + name, + Koc, + DT50_ws = NA, + DT50_soil = NA, + DT50_water = NA, + DT50_sediment = NA, + cwsat = 1000, + mw = NA, + max_soil = 1, + max_ws = 1 +) } \arguments{ \item{name}{Length one character vector containing the name} diff --git a/man/endpoint.Rd b/man/endpoint.Rd index 204905b..2b66c21 100644 --- a/man/endpoint.Rd +++ b/man/endpoint.Rd @@ -8,23 +8,39 @@ \alias{soil_sorption} \title{Retrieve endpoint information from the chyaml field of a chent object} \usage{ -endpoint(chent, medium = "soil", type = c("degradation", "sorption"), - lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", - "anaerobic"), value = c("DT50ref", "Kfoc", "N"), - aggregator = geomean, raw = FALSE, signif = 3) +endpoint( + chent, + medium = "soil", + type = c("degradation", "sorption"), + lab_field = c(NA, "laboratory", "field"), + redox = c(NA, "aerobic", "anaerobic"), + value = c("DT50ref", "Kfoc", "N"), + aggregator = geomean, + raw = FALSE, + signif = 3 +) -soil_DT50(chent, aggregator = geomean, signif = 3, - lab_field = "laboratory", value = "DT50ref", redox = "aerobic", - raw = FALSE) +soil_DT50( + chent, + aggregator = geomean, + signif = 3, + lab_field = "laboratory", + value = "DT50ref", + redox = "aerobic", + raw = FALSE +) -soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", - raw = FALSE) +soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE) soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) -soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = - geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), - raw = FALSE) +soil_sorption( + chent, + values = c("Kfoc", "N"), + aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), + signif = c(Kfoc = 3, N = 3), + raw = FALSE +) } \arguments{ \item{chent}{The chent object to get the information from} diff --git a/man/geomean.Rd b/man/geomean.Rd index 2887929..506e64d 100644 --- a/man/geomean.Rd +++ b/man/geomean.Rd @@ -4,7 +4,7 @@ \alias{geomean} \title{Calculate the geometric mean} \usage{ -geomean(x, na.rm = TRUE) +geomean(x, na.rm = FALSE) } \arguments{ \item{x}{Vector of numbers} @@ -17,8 +17,9 @@ The geometric mean \description{ Based on some posts in a thread on Stackoverflow \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0. +This function returns NA if NA values are present and na.rm = FALSE +(default). If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0. } \examples{ geomean(c(1, 3, 9)) diff --git a/man/one_box.Rd b/man/one_box.Rd index 3c34dae..a60aa39 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -11,11 +11,9 @@ one_box(x, ini, ..., t_end = 100, res = 0.01) \method{one_box}{numeric}(x, ini = 1, ..., t_end = 100, res = 0.01) -\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, - res = 0.01) +\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, res = 0.01) -\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, - res = 0.01) +\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01) } \arguments{ \item{x}{When numeric, this is the half-life to be used for an exponential diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd index fdc99fe..6684fa4 100644 --- a/man/pfm_degradation.Rd +++ b/man/pfm_degradation.Rd @@ -4,9 +4,14 @@ \alias{pfm_degradation} \title{Calculate a time course of relative concentrations based on an mkinmod model} \usage{ -pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = - log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, - by = step_days)) +pfm_degradation( + model = "SFO", + DT50 = 1000, + parms = c(k_parent_sink = log(2)/DT50), + years = 1, + step_days = 1, + times = seq(0, years * 365, by = step_days) +) } \arguments{ \item{model}{The degradation model to be used. Either a parent only model like diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd index f06d3c7..7eeb3fc 100644 --- a/man/plot.TOXSWA_cwa.Rd +++ b/man/plot.TOXSWA_cwa.Rd @@ -4,10 +4,18 @@ \alias{plot.TOXSWA_cwa} \title{Plot TOXSWA surface water concentrations} \usage{ -\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", - "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default", - add = FALSE, threshold_factor = 1000, thin_low = 1, - total = FALSE, LC_TIME = "C", ...) +\method{plot}{TOXSWA_cwa}( + x, + time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), + xlab = "default", + ylab = "default", + add = FALSE, + threshold_factor = 1000, + thin_low = 1, + total = FALSE, + LC_TIME = "C", + ... +) } \arguments{ \item{x}{The TOXSWA_cwa object to be plotted.} diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd index a212c11..35e7bf7 100644 --- a/man/plot.one_box.Rd +++ b/man/plot.one_box.Rd @@ -4,9 +4,16 @@ \alias{plot.one_box} \title{Plot time series of decline data} \usage{ -\method{plot}{one_box}(x, xlim = range(time(x)), ylim = c(0, max(x)), - xlab = "Time", ylab = "Residue", max_twa = NULL, - max_twa_var = dimnames(x)[[2]][1], ...) +\method{plot}{one_box}( + x, + xlim = range(time(x)), + ylim = c(0, max(x)), + xlab = "Time", + ylab = "Residue", + max_twa = NULL, + max_twa_var = dimnames(x)[[2]][1], + ... +) } \arguments{ \item{x}{The object of type \code{\link{one_box}} to be plotted} diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd index ccd403a..b6ee4f6 100644 --- a/man/read.TOXSWA_cwa.Rd +++ b/man/read.TOXSWA_cwa.Rd @@ -4,9 +4,16 @@ \alias{read.TOXSWA_cwa} \title{Read TOXSWA surface water concentrations} \usage{ -read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, - segment = "last", substance = "parent", total = FALSE, - windows = NULL, thresholds = NULL) +read.TOXSWA_cwa( + filename, + basedir = ".", + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE, + windows = NULL, + thresholds = NULL +) } \arguments{ \item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd index 007f00d..44ab2be 100644 --- a/man/sawtooth.Rd +++ b/man/sawtooth.Rd @@ -4,8 +4,12 @@ \alias{sawtooth} \title{Create decline time series for multiple applications} \usage{ -sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, - (n - 1) * i, length.out = n), amount = 1)) +sawtooth( + x, + n = 1, + i = 365, + applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) +) } \arguments{ \item{x}{A \code{\link{one_box}} object} diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd index 47b7e33..7135d0d 100644 --- a/man/set_nd_nq.Rd +++ b/man/set_nd_nq.Rd @@ -7,8 +7,14 @@ \usage{ set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE) -set_nd_nq_focus(res_raw, lod, loq = NA, set_first_sample_nd = TRUE, - first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE) +set_nd_nq_focus( + res_raw, + lod, + loq = NA, + set_first_sample_nd = TRUE, + first_sample_nd_value = 0, + ignore_below_loq_after_first_nd = TRUE +) } \arguments{ \item{res_raw}{Character vector of a residue time series, or matrix of diff --git a/tests/testthat/test_geomean.R b/tests/testthat/test_geomean.R index 0cc3416..bf298c2 100644 --- a/tests/testthat/test_geomean.R +++ b/tests/testthat/test_geomean.R @@ -4,8 +4,8 @@ context("Geometric mean calculation") test_that("The geometric mean is correctly calculated", { expect_equal(geomean(c(1, 3, 9)), 3) expect_equal(geomean(c(0, 3, 9)), 0) - expect_error(geomean(c(1, 3, NA, 9), na.rm = FALSE), "NA") + expect_equal(geomean(c(1, 3, NA, 9), na.rm = FALSE), NA) expect_equal(geomean(c(1, 3, NA, 9), na.rm = TRUE), 3) expect_error(geomean(c(1, -3, 9)), "positive") - expect_error(geomean(c(1, -3, NA, 9)), "positive") + expect_equal(geomean(c(1, -3, NA, 9)), NA) }) |
