diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-16 15:43:50 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-16 15:43:50 +0200 |
| commit | 36036b5901223591e7e21e8b73d8cd1fb034f4cb (patch) | |
| tree | ed8e764778aa2e94b785263d18d7d8e3dfe4e785 /docs/reference/PEC_soil.html | |
| parent | d042f8f06b313e8595087587455daac73d84f17b (diff) | |
Finish the Step 1 calculator including tests
Some cleaning up. PELMO facilities do not currently work at my end,
as I have no working wine installation on this computer
Diffstat (limited to 'docs/reference/PEC_soil.html')
| -rw-r--r-- | docs/reference/PEC_soil.html | 133 |
1 files changed, 84 insertions, 49 deletions
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 0449f8e..4b1b7b9 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -25,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -76,62 +78,95 @@ attempt is made at calculating a long term maximum concentration using the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p> - <pre><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>, + <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'>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'>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'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2015"</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> - <dl class="dl-horizontal"> - <dt>rate</dt> - <dd>Application rate in units specified below</dd> - <dt>rate_units</dt> - <dd>Defaults to g/ha</dd> - <dt>interception</dt> - <dd>The fraction of the application rate that does not reach the soil</dd> - <dt>mixing_depth</dt> - <dd>Mixing depth in cm</dd> - <dt>PEC_units</dt> - <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd> - <dt>PEC_pw_units</dt> - <dd>Only mg/L currently supported</dd> - <dt>interval</dt> - <dd>Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days</dd> - <dt>n_periods</dt> - <dd>Number of periods to be considered for long term PEC calculations</dd> - <dt>tillage_depth</dt> - <dd>Periodic (see interval) deeper mixing in cm</dd> - <dt>chent</dt> - <dd>An optional chent object holding substance specific information. Can -also be a name for the substance as a character string</dd> - <dt>DT50</dt> - <dd>If specified, overrides soil DT50 endpoints from a chent object + <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, defaults to 365, which is a year if +rate 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>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 If DT50 is not specified here and not available from the chent object, zero -degradation is assumed</dd> - <dt>Koc</dt> - <dd>If specified, overrides Koc endpoints from a chent object</dd> - <dt>Kom</dt> - <dd>Calculated from Koc by default, but can explicitly be specified -as Kom here</dd> - <dt>t_avg</dt> - <dd>Averaging times for time weighted average concentrations</dd> - <dt>scenarios</dt> - <dd>If this is 'default', the DT50 will be used without correction +degradation is assumed</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>scenarios</th> + <td><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", +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), +'chents' 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.</dd> - <dt>porewater</dt> - <dd>Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used.</p></td> + </tr> + <tr> + <th>porewater</th> + <td><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).</dd> - </dl> +p. 13).</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -140,18 +175,18 @@ p. 13).</dd> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>This assumes that the complete load to soil during the time specified by -'interval' (typically 365 days) is dosed at once. As in the PPR panel +'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion cited below (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 +<p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2015, p. 13) can easily be calculated.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>If temperature information is available in the selected scenarios, as 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> + (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> @@ -160,7 +195,7 @@ guidance (2015, p. 13) can easily be calculated.</p> selection and scenario parameterisation for predicting environmental concentrations of plant protection products in soil. <em>EFSA Journal</em> <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p> - <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for +<p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 |