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</ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> - </header><div class="row"> - <div class="contents col-md-9"> - <div class="page-header"> - <h1>Reference</h1> + + </div> +</nav><div class="container template-reference-index"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function reference</h1> </div> - <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> - <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><one_box></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="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="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> - <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="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> - <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="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> - <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><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="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> - <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><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="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> - <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="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </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> - - <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> + <div class="section level2"> + <h2 id="general-utility-functions">General utility functions<a class="anchor" aria-label="anchor" href="#general-utility-functions"></a></h2> + + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="geomean.html">geomean()</a></code> + </dt> + <dd>Calculate the geometric mean</dd> + </dl><dl><dt> + + <code><a href="one_box.html">one_box()</a></code> + </dt> + <dd>Create a time series of decline data</dd> + </dl><dl><dt> + + <code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> + </dt> + <dd>Plot time series of decline data</dd> + </dl><dl><dt> + + <code><a href="sawtooth.html">sawtooth()</a></code> + </dt> + <dd>Create decline time series for multiple applications</dd> + </dl><dl><dt> + + <code><a href="twa.html">twa()</a></code> + </dt> + <dd>Calculate a time weighted average concentration</dd> + </dl><dl><dt> + + <code><a href="max_twa.html">max_twa()</a></code> + </dt> + <dd>The maximum time weighted average concentration for a moving window</dd> + </dl><dl><dt> + + <code><a href="pfm_degradation.html">pfm_degradation()</a></code> + </dt> + <dd>Calculate a time course of relative concentrations based on an mkinmod model</dd> + </dl><dl><dt> + + <code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> + </dt> + <dd>Actual and maximum moving window time average concentrations for SFO kinetics</dd> + </dl><dl><dt> + + <code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> + </dt> + <dd>Actual and maximum moving window time average concentrations for FOMC kinetics</dd> + </dl><dl><dt> + + <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> + </dt> + <dd>Objects exported from other packages</dd> + </dl><dl><dt> + + <code><a href="TSCF.html">TSCF()</a></code> + </dt> + <dd>Estimation of the transpiration stream concentration factor</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-soil"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="PEC_soil.html">PEC_soil()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in soil</dd> + </dl><dl><dt> + + <code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> + </dt> + <dd>Calculate initial and accumulation PEC soil for a set of metabolites</dd> + </dl><dl><dt> + + <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> + </dt> + <dd>Properties of the predefined scenarios from the EFSA guidance from 2015</dd> + </dl><dl><dt> + + <code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> + </dt> + <dd>Properties of the predefined scenarios from the EFSA guidance from 2017</dd> + </dl><dl><dt> + + <code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> + </dt> + <dd>Get the relative accumulation of an FOMC model over multiples of an interval</dd> + </dl><dl><dt> + + <code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> + </dt> + <dd>Subset of EFSA crop washoff default values</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-groundwater"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> + </dt> + <dd>A very small subset of the FOCUS Groundwater scenario definitions</dd> + </dl><dl><dt> + + <code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> + </dt> + <dd>Subset of EFSA crop interception default values for groundwater modelling</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-surface-water"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in surface water due to drift</dd> + </dl><dl><dt> + + <code><a href="drift_data_JKI.html">drift_data_JKI</a></code> + </dt> + <dd>Deposition from spray drift expressed as percent of the applied dose as +published by the JKI</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> + </dt> + <dd>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in sediment from surface +water concentrations</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> + </dt> + <dd>Calculate PEC surface water at FOCUS Step 1</dd> + </dl><dl><dt> + + <code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> + </dt> + <dd>Create a chemical compound object for FOCUS Step 1 calculations</dd> + </dl><dl><dt> + + <code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> + </dt> + <dd>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> + </dt> + <dd>Calculate PEC surface water due to drainage as in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> + </dt> + <dd>Calculate PEC surface water due to runoff and erosion as in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> + </dt> + <dd>Runoff loss percentages as used in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> + </dt> + <dd>Runoff reduction percentages as used in Exposit</dd> + </dl><dl><dt> + + <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> + </dt> + <dd>R6 class for holding TOXSWA water concentration data and associated statistics</dd> + </dl><dl><dt> + + <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> + </dt> + <dd>Read TOXSWA surface water concentrations</dd> + </dl><dl><dt> + + <code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> + </dt> + <dd>Plot TOXSWA surface water concentrations</dd> + </dl></div><div class="section level2"> + <h2 id="classifications-and-indicators">Classifications and indicators<a class="anchor" aria-label="anchor" href="#classifications-and-indicators"></a></h2> + + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> + </dt> + <dd>Determine the SSLRC mobility classification for a chemical substance from its Koc</dd> + </dl><dl><dt> + + <code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> + </dt> + <dd>Groundwater ubiquity score based on Gustafson (1989)</dd> + </dl></div><div class="section level2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information<a class="anchor" aria-label="anchor" href="#work-with-chent-objects-containing-relevant-information"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <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> + </dt> + <dd>Retrieve endpoint information from the chyaml field of a chent object</dd> + </dl></div><div class="section level2"> + <h2 id="utilities">Utilities<a class="anchor" aria-label="anchor" href="#utilities"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + <dl><dt> + + <code><a href="get_vertex.html">get_vertex()</a></code> + </dt> + <dd>Fit a parabola through three points</dd> + </dl></div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <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> |