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| -rw-r--r-- | docs/reference/reexports.html | 83 |
5 files changed, 793 insertions, 1066 deletions
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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)." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +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><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,35 +21,21 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in soil</h1> @@ -117,164 +51,167 @@ 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>, - <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> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>mixing_depth</th> - <td><p>Mixing depth in cm</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></td> - </tr> - <tr> - <th>PEC_pw_units</th> - <td><p>Only mg/L currently supported</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Period of the deeper mixing. The default is NA, i.e. no + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> mixing_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"mg/kg"</span>,</span> +<span> PEC_pw_units <span class="op">=</span> <span class="st">"mg/L"</span>,</span> +<span> interval <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> n_periods <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> tillage_depth <span class="op">=</span> <span class="fl">20</span>,</span> +<span> leaching_depth <span class="op">=</span> <span class="va">tillage_depth</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"annual"</span>,</span> +<span> cultivation <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> chent <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> FOMC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Kom <span class="op">=</span> <span class="va">Koc</span><span class="op">/</span><span class="fl">1.724</span>,</span> +<span> t_avg <span class="op">=</span> <span class="fl">0</span>,</span> +<span> t_act <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> scenarios <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"default"</span>, <span class="st">"EFSA_2017"</span>, <span class="st">"EFSA_2015"</span><span class="op">)</span>,</span> +<span> leaching <span class="op">=</span> <span class="va">scenarios</span> <span class="op">==</span> <span class="st">"EFSA_2017"</span>,</span> +<span> porewater <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> + + +<dt>mixing_depth</dt> +<dd><p>Mixing depth in cm</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></dd> + + +<dt>PEC_pw_units</dt> +<dd><p>Only mg/L currently supported</p></dd> + + +<dt>interval</dt> +<dd><p>Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation -units are in days</p></td> - </tr> - <tr> - <th>n_periods</th> - <td><p>Number of periods to be considered for long term PEC calculations</p></td> - </tr> - <tr> - <th>tillage_depth</th> - <td><p>Periodic (see interval) deeper mixing in cm</p></td> - </tr> - <tr> - <th>leaching_depth</th> - <td><p>EFSA (2017) uses the mixing depth (ecotoxicological +units are in days</p></dd> + + +<dt>n_periods</dt> +<dd><p>Number of periods to be considered for long term PEC calculations</p></dd> + + +<dt>tillage_depth</dt> +<dd><p>Periodic (see interval) deeper mixing in cm</p></dd> + + +<dt>leaching_depth</dt> +<dd><p>EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage -depth are taken into account in this implementation.</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Ignored for scenarios other than EFSA_2017. Only annual crops +depth are taken into account in this implementation.</p></dd> + + +<dt>crop</dt> +<dd><p>Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping -cycle per year are currently supported.</p></td> - </tr> - <tr> - <th>cultivation</th> - <td><p>Does mechanical cultivation in the sense of EFSA (2017) +cycle per year are currently supported.</p></dd> + + +<dt>cultivation</dt> +<dd><p>Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios -other than EFSA_2017</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>An optional chent object holding substance specific information. Can -also be a name for the substance as a character string</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>If specified, overrides soil DT50 endpoints from a chent object +other than EFSA_2017</p></dd> + + +<dt>chent</dt> +<dd><p>An optional chent object holding substance specific information. Can +also be a name for the substance as a character string</p></dd> + + +<dt>DT50</dt> +<dd><p>If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero -degradation is assumed</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>If specified, it should be a named numeric vector containing +degradation is assumed</p></dd> + + +<dt>FOMC</dt> +<dd><p>If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC -is calculated using these parameters without temperature correction</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>If specified, overrides Koc endpoints from a chent object</p></td> - </tr> - <tr> - <th>Kom</th> - <td><p>Calculated from Koc by default, but can explicitly be specified -as Kom here</p></td> - </tr> - <tr> - <th>t_avg</th> - <td><p>Averaging times for time weighted average concentrations</p></td> - </tr> - <tr> - <th>t_act</th> - <td><p>Time series for actual concentrations</p></td> - </tr> - <tr> - <th>scenarios</th> - <td><p>If this is 'default', the DT50 will be used without correction +is calculated using these parameters without temperature correction</p></dd> + + +<dt>Koc</dt> +<dd><p>If specified, overrides Koc endpoints from a chent object</p></dd> + + +<dt>Kom</dt> +<dd><p>Calculated from Koc by default, but can explicitly be specified +as Kom here</p></dd> + + +<dt>t_avg</dt> +<dd><p>Averaging times for time weighted average concentrations</p></dd> + + +<dt>t_act</dt> +<dd><p>Time series for actual concentrations</p></dd> + + +<dt>scenarios</dt> +<dd><p>If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), +'chent' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.</p></td> - </tr> - <tr> - <th>leaching</th> - <td><p>Should leaching be taken into account? The default is FALSE, -except when the EFSA_2017 scenarios are used.</p></td> - </tr> - <tr> - <th>porewater</th> - <td><p>Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used.</p></dd> + + +<dt>leaching</dt> +<dd><p>Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.</p></dd> + + +<dt>porewater</dt> +<dd><p>Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).</p></td> - </tr> - </table> +p. 13).</p></dd> - <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> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The predicted concentration in soil</p> + </div> + <div id="details"> + <h2>Details</h2> <p>This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel 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> - + </div> + <div id="note"> + <h2>Note</h2> <p>While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -289,8 +226,9 @@ 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> - + </div> + <div id="references"> + <h2>References</h2> <p>EFSA Panel on Plant Protection Products and their Residues (2012) Scientific Opinion on the science behind the guidance for scenario selection and scenario parameterisation for predicting environmental @@ -306,75 +244,80 @@ 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 -#> t_avg default -#> 0 0.1</div><div class='input'> -<span class='co'># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span> -<span class='co'># Note that TWA concentrations differ from the ones given in the guidance</span> -<span class='co'># for an unknown reason (the values from EFSA (2015) can be reproduced).</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</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'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 19.76834 13.8619 10.53795 -#> 21 19.59345 13.7169 10.39882</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</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'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.5541984 0.6779249 0.9816693 -#> 21 0.5484576 0.6693125 0.9609119</div><div class='input'> -<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</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'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 21.96827 11.53750 9.145259 -#> 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</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'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.7589401 0.6674322 0.9147861 -#> 21 0.7506036 0.6590345 0.8987279</div><div class='input'> -<span class='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> -<span class='co'># Metabolite M2</span> -<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span> -<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> -<span class='no'>results_pfm</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</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'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>) -<span class='no'>results_pfm_pw</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</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'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</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="#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> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg default</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span></span></span> +<span class="r-in"><span><span class="co"># Note that TWA concentrations differ from the ones given in the guidance</span></span></span> +<span class="r-in"><span><span class="co"># for an unknown reason (the values from EFSA (2015) can be reproduced).</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 19.76834 13.8619 10.53795</span> +<span class="r-out co"><span class="r-pr">#></span> 21 19.59345 13.7169 10.39882</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.5541984 0.6779249 0.9816693</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.5484576 0.6693125 0.9609119</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 21.96827 11.53750 9.145259</span> +<span class="r-out co"><span class="r-pr">#></span> 21 21.78517 11.40701 9.017370</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.7589401 0.6674322 0.9147861</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.7506036 0.6590345 0.8987279</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="co"># Metabolite M2</span></span></span> +<span class="r-in"><span><span class="co"># Calculate total and porewater soil concentrations for tier 1 scenarios</span></span></span> +<span class="r-in"><span><span class="co"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span></span></span> +<span class="r-in"><span><span class="va">results_pfm</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">results_pfm_pw</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> 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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 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." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +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><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,35 +23,21 @@ to be used with the FOCUS calculator." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water at FOCUS Step 1</h1> @@ -121,115 +55,114 @@ 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> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>parent</th> - <td><p>A list containing substance specific parameters, e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>.</p></td> - </tr> - <tr> - <th>rate</th> - <td><p>The application rate in g/ha. Overriden when -applications are given explicitly</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The application interval</p></td> - </tr> - <tr> - <th>comment</th> - <td><p>A comment for the input file</p></td> - </tr> - <tr> - <th>met</th> - <td><p>A list containing metabolite specific parameters. e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>. If not NULL, -the PEC is calculated for this compound, not the parent.</p></td> - </tr> - <tr> - <th>f_drift</th> - <td><p>The fraction of the application rate reaching the waterbody + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_focus</span><span class="op">(</span></span> +<span> <span class="va">parent</span>,</span> +<span> <span class="va">rate</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> comment <span class="op">=</span> <span class="st">""</span>,</span> +<span> met <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> f_drift <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> f_rd <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> scenario <span class="op">=</span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span>,</span> +<span> region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"n"</span>, <span class="st">"s"</span><span class="op">)</span>,</span> +<span> season <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"of"</span>, <span class="st">"mm"</span>, <span class="st">"js"</span><span class="op">)</span>,</span> +<span> interception <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"no interception"</span>, <span class="st">"minimal crop cover"</span>, <span class="st">"average crop cover"</span>,</span> +<span> <span class="st">"full canopy"</span><span class="op">)</span>,</span> +<span> met_form_water <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> txt_file <span class="op">=</span> <span class="st">"pesticide.txt"</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> append <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>parent</dt> +<dd><p>A list containing substance specific parameters, e.g. +conveniently generated by [chent_focus_sw].</p></dd> + + +<dt>rate</dt> +<dd><p>The application rate in g/ha. Overriden when +applications are given explicitly</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications</p></dd> + + +<dt>i</dt> +<dd><p>The application interval</p></dd> + + +<dt>comment</dt> +<dd><p>A comment for the input file</p></dd> + + +<dt>met</dt> +<dd><p>A list containing metabolite specific parameters. e.g. +conveniently generated by [chent_focus_sw]. If not NULL, +the PEC is calculated for this compound, not the parent.</p></dd> + + +<dt>f_drift</dt> +<dd><p>The fraction of the application rate reaching the waterbody via drift. If NA, this is derived from the scenario name and the number of applications via the drift data defined by the -<code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>f_rd</th> - <td><p>The fraction of the amount applied reaching the waterbody via +[FOCUS_Step_12_scenarios]</p></dd> + + +<dt>f_rd</dt> +<dd><p>The fraction of the amount applied reaching the waterbody via runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the --> -parent or a metabolite</p></td> - </tr> - <tr> - <th>scenario</th> - <td><p>The name of the scenario. Must be one of the scenario -names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>region</th> - <td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only -Step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>season</th> - <td><p>'of' for October to February, 'mm' for March to May, and 'js' -for June to September. If NA, only step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>One of 'no interception' (default), 'minimal crop cover', -'average crop cover' or 'full canopy'</p></td> - </tr> - <tr> - <th>met_form_water</th> - <td><p>Should the metabolite formation in water be taken into +parent or a metabolite</p></dd> + + +<dt>scenario</dt> +<dd><p>The name of the scenario. Must be one of the scenario +names given in [FOCUS_Step_12_scenarios]</p></dd> + + +<dt>region</dt> +<dd><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated</p></dd> + + +<dt>season</dt> +<dd><p>'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated</p></dd> + + +<dt>interception</dt> +<dd><p>One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'</p></dd> + + +<dt>met_form_water</dt> +<dd><p>Should the metabolite formation in water be taken into account? This can be switched off to check the influence and to compare -with previous versions of the Steps 12 calculator</p></td> - </tr> - <tr> - <th>txt_file</th> - <td><p>the name, and potentially the full path to the +with previous versions of the Steps 12 calculator</p></dd> + + +<dt>txt_file</dt> +<dd><p>the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) -should be written</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>Should an existing file a the location specified in -<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></td> - </tr> - <tr> - <th>append</th> - <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> +should be written</p></dd> + + +<dt>overwrite</dt> +<dd><p>Should an existing file a the location specified in +<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></dd> + +<dt>append</dt> +<dd><p>Should the input text file be appended?</p></dd> + +</dl></div> + <div id="note"> + <h2>Note</h2> <p>The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -237,142 +170,141 @@ 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> - + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p> <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> + </div> - <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> -<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> $f_drift -#> [1] 0 -#> -#> $eq_rate_drift_s -#> [1] 3000 -#> -#> $eq_rate_rd_s -#> [1] 3000 -#> -#> $eq_rate_rd_parent_s -#> [1] NA -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 300 -#> -#> $f_rd_sw -#> [1] 0.6850566 -#> -#> $f_rd_sed -#> [1] 0.3149434 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 6.850566e+02 NA 2.362075e+03 NA -#> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 -#> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 -#> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 -#> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 -#> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 -#> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 -#> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 -#> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 -#> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 -#> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 -#> -#> $PEC_sw_max -#> [1] 685.0566 -#> -#> $PEC_sed_max -#> [1] 2362.075 -#> </div><div class='input'> -<span class='co'># Metabolite</span> -<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>) -<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, - <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#> $f_drift -#> [1] 0.02759 -#> -#> $eq_rate_drift_s -#> [1] 0 -#> -#> $eq_rate_rd_s -#> [1] 200 -#> -#> $eq_rate_rd_parent_s -#> [1] 0 -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 20 -#> -#> $f_rd_sw -#> [1] 0.9375 -#> -#> $f_rd_sed -#> [1] 0.0625 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 62.50000 NA 31.25000 NA -#> 1 62.06828 62.28414 31.03414 31.14207 -#> 2 61.63954 62.06890 30.81977 31.03445 -#> 4 60.79093 61.64158 30.39547 30.82079 -#> 7 59.53987 61.00800 29.76994 30.50400 -#> 14 56.71995 59.56326 28.35997 29.78163 -#> 21 54.03358 58.16414 27.01679 29.08207 -#> 28 51.47444 56.80902 25.73722 28.40451 -#> 42 46.71404 54.22460 23.35702 27.11230 -#> 50 44.19417 52.81945 22.09709 26.40973 -#> 100 31.25000 45.08422 15.62500 22.54211 -#> -#> $PEC_sw_max -#> [1] 62.5 -#> -#> $PEC_sed_max -#> [1] 31.25 -#> </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="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span> +<span class="r-in"><span><span class="va">dummy_1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, append <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 300</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.6850566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.3149434</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 6.850566e+02 NA 2.362075e+03 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225</span> +<span class="r-out co"><span class="r-pr">#></span> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255</span> +<span class="r-out co"><span class="r-pr">#></span> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592</span> +<span class="r-out co"><span class="r-pr">#></span> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501</span> +<span class="r-out co"><span class="r-pr">#></span> 21 6.055102e+01 257.45458 2.087799e+02 887.7034</span> +<span class="r-out co"><span class="r-pr">#></span> 28 2.697241e+01 203.47173 9.300089e+01 701.5705</span> +<span class="r-out co"><span class="r-pr">#></span> 42 5.352005e+00 140.10377 1.845371e+01 483.0778</span> +<span class="r-out co"><span class="r-pr">#></span> 50 2.123945e+00 118.24602 7.323361e+00 407.7123</span> +<span class="r-out co"><span class="r-pr">#></span> 100 6.585062e-03 59.30629 2.270529e-02 204.4881</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 685.0566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 2362.075</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Metabolite</span></span></span> +<span class="r-in"><span><span class="va">new_dummy</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"New Dummy"</span>, mw <span class="op">=</span> <span class="fl">250</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">M1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"M1"</span>, mw <span class="op">=</span> <span class="fl">100</span>, cwsat <span class="op">=</span> <span class="fl">100</span>, DT50_ws <span class="op">=</span> <span class="fl">100</span>, Koc <span class="op">=</span> <span class="fl">50</span>,</span></span> +<span class="r-in"><span> max_ws <span class="op">=</span> <span class="fl">0</span>, max_soil <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">new_dummy</span>, <span class="fl">1000</span>, scenario <span class="op">=</span> <span class="st">"cereals, winter"</span>, met <span class="op">=</span> <span class="va">M1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.02759</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 200</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 20</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.9375</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 62.50000 NA 31.25000 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 62.06828 62.28414 31.03414 31.14207</span> +<span class="r-out co"><span class="r-pr">#></span> 2 61.63954 62.06890 30.81977 31.03445</span> +<span class="r-out co"><span class="r-pr">#></span> 4 60.79093 61.64158 30.39547 30.82079</span> +<span class="r-out co"><span class="r-pr">#></span> 7 59.53987 61.00800 29.76994 30.50400</span> +<span class="r-out co"><span class="r-pr">#></span> 14 56.71995 59.56326 28.35997 29.78163</span> +<span class="r-out co"><span class="r-pr">#></span> 21 54.03358 58.16414 27.01679 29.08207</span> +<span class="r-out co"><span class="r-pr">#></span> 28 51.47444 56.80902 25.73722 28.40451</span> +<span class="r-out co"><span class="r-pr">#></span> 42 46.71404 54.22460 23.35702 27.11230</span> +<span class="r-out co"><span class="r-pr">#></span> 50 44.19417 52.81945 22.09709 26.40973</span> +<span class="r-out co"><span class="r-pr">#></span> 100 31.25000 45.08422 15.62500 22.54211</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 62.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 31.25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git 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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. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by read.TOXSWA_cwa." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +by read.TOXSWA_cwa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,35 +21,21 @@ by read.TOXSWA_cwa." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> @@ -117,179 +48,236 @@ by read.TOXSWA_cwa." /> and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> +by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object.</p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> + <p></p><div class="r6-fields"><dl><dt><code>filename</code></dt> +<dd><p>Length one character vector holding the filename.</p></dd> - <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="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>basedir</code></dt> +<dd><p>Length one character vector holding the directory where the file came from.</p></dd> + - <p><div class="r6-fields"></p><dl'> -<dt><code>filename</code></dt><dd><p>Length one character vector holding the filename.</p></dd> +<dt><code>zipfile</code></dt> +<dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> -<dt><code>basedir</code></dt><dd><p>Length one character vector holding the directory where the file came from.</p></dd> -<dt><code>zipfile</code></dt><dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> +<dt><code>segment</code></dt> +<dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>substance</code></dt><dd><p>The TOXSWA name of the substance.</p></dd> +<dt><code>substance</code></dt> +<dd><p>The TOXSWA name of the substance.</p></dd> -<dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> +<dt><code>cwas</code></dt> +<dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>windows</code></dt><dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) + +<dt><code>events</code></dt> +<dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> + + +<dt><code>windows</code></dt> +<dd><p>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.</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> -<h3>Public methods</h3> - -<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> -<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>( - <span class='no'>filename</span>, - <span class='no'>basedir</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>filename</code></dt><dd><p>The filename</p></dd> - -<dt><code>basedir</code></dt><dd><p>The directory to look in</p></dd> - -<dt><code>zipfile</code></dt><dd><p>Optional path to a zipfile holding the file</p></dd> - -<dt><code>segment</code></dt><dd><p>Either "last" or the number of the segment for which to read the data</p></dd> - -<dt><code>substance</code></dt><dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> - -<dt><code>total</code></dt><dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> - -</dl><p></div></p> -<p><hr> -<a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> -<p>Add to the `windows` field described above.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>windows</code></dt><dd><p>Window sizes in days</p></dd> - -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<div class="section"> +<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> + +<ul><li><p><a href="#method-TOXSWA_cwa-new"><code>TOXSWA_cwa$new()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-moving_windows"><code>TOXSWA_cwa$moving_windows()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-get_events"><code>TOXSWA_cwa$get_events()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-print"><code>TOXSWA_cwa$print()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-clone"><code>TOXSWA_cwa$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-TOXSWA_cwa-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Create a TOXSWA_cwa object from a file</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> <span class="va">basedir</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<p></p><div class="arguments"><dl><dt><code>filename</code></dt> +<dd><p>The filename</p></dd> + + +<dt><code>basedir</code></dt> +<dd><p>The directory to look in</p></dd> + + +<dt><code>zipfile</code></dt> +<dd><p>Optional path to a zipfile holding the file</p></dd> + + +<dt><code>segment</code></dt> +<dd><p>Either "last" or the number of the segment for which to read the data</p></dd> + + +<dt><code>substance</code></dt> +<dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> + + +<dt><code>total</code></dt> +<dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> +<h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3> +<p>Add to the `windows` field described above.</p><div class="section"> +<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>windows</code></dt> +<dd><p>Window sizes in days</p></dd> + + +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> +<h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the `events` -field of the object.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +field of the object.</p><div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> +<p></p><div class="arguments"><dl><dt><code>thresholds</code></dt> +<dd><p>Threshold values in µg/L.</p></dd> -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>thresholds</code></dt><dd><p>Threshold values in µg/L.</p></dd> -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> -<p>Print a `TOXSWA_cwa` object</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</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><span class='no'>TOXSWA_cwa</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> - -</dl><p></div></p> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>10</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>)) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 -#> datetime t t_firstjan t_rel_to_max cwa_mug_per_L -#> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 -#> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 -#> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 -#> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 -#> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 -#> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 -#> cwa_tot_mug_per_L -#> 20 0 -#> 40 0 -#> 60 0 -#> 80 0 -#> 100 0 -#> 120 0 -#> Moving window analysis -#> window max_TWAC max_AUC_h max_AUC_d -#> 1 7 days 2.3926551 401.9660 16.74859 -#> 2 21 days 0.8369248 421.8101 17.57542 -#> Event statistics for threshold 2 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 -#> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 -#> Event statistics for threshold 10 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</div></pre> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> +<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> +<p>Print a `TOXSWA_cwa` object</p><div class="section"> +<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> + + +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span> +<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span> +<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 0</span> +<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span> +<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span> +<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span> +<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" 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href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> - <table class="ref-index"> - - <colgroup> - - <col class="alias" /> - <col class="title" /> - </colgroup> - - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> - <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="general-utility-functions">General utility functions <a href="#general-utility-functions" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="geomean.html">geomean()</a></code> </p> </td> <td><p>Calculate the geometric mean</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="one_box.html">one_box()</a></code> </p> </td> <td><p>Create a time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p> </td> <td><p>Plot time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="sawtooth.html">sawtooth()</a></code> </p> </td> <td><p>Create decline time series for multiple applications</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="twa.html">twa()</a></code> </p> </td> <td><p>Calculate a time weighted average concentration</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="max_twa.html">max_twa()</a></code> </p> </td> <td><p>The maximum time weighted average concentration for a moving window</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p> </td> <td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> - </tr><tr> - - <td> - <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> - </td> - <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> - </tr><tr> - - <td> + </tr><tr><td> + <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </p> + </td> + <td><p>Objects exported from other packages</p></td> + </tr><tr><td> <p><code><a href="TSCF.html">TSCF()</a></code> </p> </td> <td><p>Estimation of the transpiration stream concentration factor</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil <a href="#predicted-environmental-concentrations-in-soil" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in soil</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p> </td> <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> </td> <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> </td> <td><p>Subset of EFSA crop washoff default values</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater <a href="#predicted-environmental-concentrations-in-groundwater" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> </td> <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> </td> <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water <a href="#predicted-environmental-concentrations-in-surface-water" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> </td> <td><p>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p> </td> <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in sediment from surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p> </td> <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p> </td> <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p> </td> <td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p> </td> <td><p>Calculate PEC surface water due to drainage as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p> </td> <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p> </td> <td><p>Runoff loss percentages as used in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p> </td> <td><p>Runoff reduction percentages as used in Exposit</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> </td> <td><p>R6 class for holding TOXSWA water concentration data and associated statistics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p> </td> <td><p>Read TOXSWA surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p> </td> <td><p>Plot TOXSWA surface water concentrations</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> - <p class="section-desc"><p>Evaluating environmental fate properties</p></p> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="classifications-and-indicators">Classifications and indicators <a href="#classifications-and-indicators" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p> </td> <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p> </td> <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-work-with-chent-objects-containing-relevant-information" class="hasAnchor"><a href="#section-work-with-chent-objects-containing-relevant-information" class="anchor"></a>Work with chent objects containing relevant information</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information <a href="#work-with-chent-objects-containing-relevant-information" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> </td> <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="get_vertex.html">get_vertex()</a></code> </p> </td> <td><p>Fit a parabola through three points</p></td> - </tr> - </tbody> - </table> - </div> + </tr></tbody></table></div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html new file mode 100644 index 0000000..2f410e4 --- /dev/null +++ b/docs/reference/reexports.html @@ -0,0 +1,83 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Objects exported from other packages — reexports • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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Follow the links +below to see their documentation. + + mkin +set_nd_nq, set_nd_nq_focus + + +"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Objects exported from other packages</h1> + + <div class="hidden name"><code>reexports.Rd</code></div> + </div> + + <div class="ref-description"> + <p>These objects are imported from other packages. Follow the links +below to see their documentation.</p> +<dl><dt>mkin</dt> +<dd><p><code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq</a></code>, <code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq_focus</a></code></p></dd> + + +</dl></div> + + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + |