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diff --git a/docs/reference/index.html b/docs/reference/index.html index aaa499d..97f59b5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,337 +1,365 @@ <!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, shrink-to-fit=no"><title>Function reference • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- 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> +<!-- 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, shrink-to-fit=no"><title>Package index • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.2</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </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 class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </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> + + <h1>Package index</h1> </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"> - - - + <div class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="geomean.html">geomean()</a></code> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="PEC_soil.html">PEC_soil()</a></code> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> + + <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> + + <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"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> + + <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> + + <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> + <dd>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</dd> </dl><dl><dt> - - <code><a href="drift_parameters_focus.html">drift_parameters_focus</a></code> + + <code><a href="drift_parameters_focus.html">drift_parameters_focus</a></code> + </dt> <dd>Regression parameters for the Rautmann drift data</dd> </dl><dl><dt> - - <code><a href="drift_percentages_rautmann.html">drift_percentages_rautmann()</a></code> + + <code><a href="drift_percentages_rautmann.html">drift_percentages_rautmann()</a></code> + </dt> <dd>Calculate drift percentages based on Rautmann data</dd> </dl><dl><dt> - - <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> + + <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> + + <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> + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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> + + <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"> - - - + <div class="section-desc"><p>Evaluating environmental fate properties</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> + + <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> + + <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"> - - - + + + + </div><div 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> + + <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"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="get_vertex.html">get_vertex()</a></code> + + <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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <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> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> |