diff options
| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:16:17 +0100 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:27:50 +0100 |
| commit | aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 (patch) | |
| tree | 7ca136834857c12449f50a1e086a589cc9b79e2e /docs/reference/index.html | |
| parent | 64f629efbe666bae56f48a309adf33d1eb09c358 (diff) | |
Reorganise data generation
- Use inst/data_generation for R code generating data as in some of my other packages
- data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff
contents were not changed
- Remove ChangeLog, the history is in the git logs
- Update docs and some links contained therein
- use \doi{} markup
- Move logs to log directory
Diffstat (limited to 'docs/reference/index.html')
| -rw-r--r-- | docs/reference/index.html | 365 |
1 files changed, 73 insertions, 292 deletions
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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-index"> - <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"> @@ -71,391 +17,226 @@ </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">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</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> |