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| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-27 10:00:15 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-27 11:08:53 +0200 |
| commit | 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b (patch) | |
| tree | bd47fa18a307349eabf4ecfff7ea8da81f5bb654 /docs/reference/PELMO_runs.html | |
| parent | 803fe13e505960fddccdbd4dcb524715f5eb068d (diff) | |
Fix for UK drainage, some EFSA interception and washoff
- PEC_sw_drainage_UK() gave results that were a little bit too high
for the substances with the highest Koc (>4000), as I used 0.01% instead
of 0.008% for them. This must have come from an old vesion of the UK
data requirements handbook, at least I do not have another explanation
- Add EFSA interception (from 2014 DegT50 guidance) and tier 1
crop wash-off factors (from 2017 PEC soil guidance) for some major
arable crops
- Update docs
Diffstat (limited to 'docs/reference/PELMO_runs.html')
| -rw-r--r-- | docs/reference/PELMO_runs.html | 282 |
1 files changed, 0 insertions, 282 deletions
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html deleted file mode 100644 index 2a75191..0000000 --- a/docs/reference/PELMO_runs.html +++ /dev/null @@ -1,282 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Set up runs for FOCUS PELMO — PELMO_runs • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" /> - -<meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the install_PELMO from the PELMO.installeR package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of PELMO.installeR -and run using wine." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<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> - <div class="container template-reference-topic"> - <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"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Set up runs for FOCUS PELMO</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>PELMO_runs.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the <code>install_PELMO</code> from the <code>PELMO.installeR</code> package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of <code>PELMO.installeR</code> -and run using <code>wine</code>.</p> - - </div> - - <pre class="usage"><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>run_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>)) - -<span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>runs</th> - <td><p>A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in <code><a href='FOCUS_PELMO_crops.html'>FOCUS_PELMO_crops</a></code>, -that hold character vectors of three letter scenario acronyms -as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</p></td> - </tr> - <tr> - <th>psm_dir</th> - <td><p>The directory where the psm files are located</p></td> - </tr> - <tr> - <th>version</th> - <td><p>The FOCUS PELMO version</p></td> - </tr> - <tr> - <th>PELMO_base</th> - <td><p>Where the FOCUS PELMO installation is located</p></td> - </tr> - <tr> - <th>execute</th> - <td><p>Should PELMO be executed directly?</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to execute PELMO runs in parallel</p></td> - </tr> - <tr> - <th>evaluate</th> - <td><p>Should the results be returned?</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>Should existing run directories be overwritten?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>If evaluate is TRUE, a list of lists of matrices holding the - PEC data.</p> - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>As a side effect, an R data file (period_pfm.rda) is generated in each -run directory, holding the results for all FOCUS periods, equivalent to -the period.plm file generated by the FOCUS PELMO GUI.</p> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>PELMO.installeR <a href='https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p> -<p>Wine <a href='https://winehq.org'>https://winehq.org</a></p> -<p>PELMO test results <a href='http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Reproduce the official test results for annual application of Pesticide D</span> -<span class='co'># to winter cereals at the day before emergence</span> -<span class='no'>runs_1</span> <span class='kw'><-</span> <span class='fu'>list</span>( - <span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D'</span>, - <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>)), - <span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_day_pre_em_every_third_year'</span>, - <span class='kw'>pot</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>))) -<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>( - <span class='no'>PECgw_1</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_1</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>), - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>15</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -) -<span class='fu'>print</span>(<span class='no'>PECgw_1</span>)</div><div class='output co'>#> $Pesticide_D -#> $Pesticide_D$win -#> FOCUS DUMMY D -#> Cha 0.025 -#> Ham 1.621 -#> Jok 0.388 -#> Kre 0.467 -#> Oke 1.608 -#> Pia 0.848 -#> Por 2.386 -#> Sev 0.009 -#> Thi 0.030 -#> -#> -#> $Pesticide_D_1_day_pre_em_every_third_year -#> $Pesticide_D_1_day_pre_em_every_third_year$pot -#> FOCUS DUMMY D -#> Cha 0.010 -#> Ham 0.014 -#> Jok 0.009 -#> Kre 0.027 -#> Oke 0.085 -#> Pia 0.051 -#> Por 0.021 -#> Sev 0.000 -#> Thi 0.001 -#> -#> </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span> -<span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#> User System verstrichen -#> 0.395 0.093 30.590 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'><-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) { - <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]])) -}</div><div class='output co'>#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'> -<span class='co'># Demonstrate some results with metabolites.</span> -<span class='no'>runs_2</span> <span class='kw'><-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>, - <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>))) -<span class='no'>PECgw_2</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_2</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>), - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>print</span>(<span class='no'>PECgw_2</span>)</div><div class='output co'>#> $Pesticide_D_1_May_every_other_year_mets -#> $Pesticide_D_1_May_every_other_year_mets$win -#> FOCUS DUMMY D M1 M2 -#> Cha 0.001 126.195 0.000 -#> Ham 0.054 82.196 0.001 -#> Kre 0.103 75.494 0.001 -#> -#> </div></pre> - </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="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - - <li><a href="#details">Details</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - 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