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      <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>
        </th>
      </tr>
      <tr>
        
        <td>
          <p><code><a href="geomean.html">geomean()</a></code> </p>
        </td>
        <td><p>Calculate the geometric mean</p></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>
          <p><code><a href="plot.one_box.html">plot(<i>&lt;one_box&gt;</i>)</a></code> </p>
        </td>
        <td><p>Plot time series of decline data</p></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>
          <p><code><a href="twa.html">twa()</a></code> </p>
        </td>
        <td><p>Calculate a time weighted average concentration</p></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>
          <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>
          <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>
          <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
This function automates replacing unquantified values in residue time and
depth series. For time series, the function performs part of the residue
processing proposed in the FOCUS kinetics guidance for parent compounds
and metabolites. For two-dimensional residue series over time and depth,
it automates the proposal of Boesten et al (2015).</p></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>
          <p class="section-desc"></p>
        </th>
      </tr>
      <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <p class="section-desc"></p>
        </th>
      </tr>
      <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>
          <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>
          <p class="section-desc"></p>
        </th>
      </tr>
      <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <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>
          <p><code><a href="plot.TOXSWA_cwa.html">plot(<i>&lt;TOXSWA_cwa&gt;</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>
        </th>
      </tr>
      <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>
          <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i>&lt;GUS_result&gt;</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-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2>
          <p class="section-desc"></p>
        </th>
      </tr>
      <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>

  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#section-general-utility-functions">General utility functions</a></li>
      <li><a href="#section-predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil</a></li>
      <li><a href="#section-predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater</a></li>
      <li><a href="#section-predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water</a></li>
      <li><a href="#section-classifications-and-indicators">Classifications and indicators</a></li>
      <li><a href="#section-utilities">Utilities</a></li>
    </ul>
  </div>
</div>


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