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authorJohannes Ranke <jranke@uni-bremen.de>2019-09-27 10:00:15 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-09-27 11:08:53 +0200
commit435e07a6f7fd2599d783fd306ee6d9e08acc0c6b (patch)
treebd47fa18a307349eabf4ecfff7ea8da81f5bb654 /docs/reference/PELMO_runs.html
parent803fe13e505960fddccdbd4dcb524715f5eb068d (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
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- <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'>&lt;-</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'>&lt;-</span> <span class='fu'>system.time</span>(
- <span class='no'>PECgw_1</span> <span class='kw'>&lt;-</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'>#&gt; $Pesticide_D
-#&gt; $Pesticide_D$win
-#&gt; FOCUS DUMMY D
-#&gt; Cha 0.025
-#&gt; Ham 1.621
-#&gt; Jok 0.388
-#&gt; Kre 0.467
-#&gt; Oke 1.608
-#&gt; Pia 0.848
-#&gt; Por 2.386
-#&gt; Sev 0.009
-#&gt; Thi 0.030
-#&gt;
-#&gt;
-#&gt; $Pesticide_D_1_day_pre_em_every_third_year
-#&gt; $Pesticide_D_1_day_pre_em_every_third_year$pot
-#&gt; FOCUS DUMMY D
-#&gt; Cha 0.010
-#&gt; Ham 0.014
-#&gt; Jok 0.009
-#&gt; Kre 0.027
-#&gt; Oke 0.085
-#&gt; Pia 0.051
-#&gt; Por 0.021
-#&gt; Sev 0.000
-#&gt; Thi 0.001
-#&gt;
-#&gt; </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'>#&gt; User System verstrichen
-#&gt; 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'>&lt;-</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'>#&gt; 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'>&lt;-</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'>&lt;-</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'>#&gt; $Pesticide_D_1_May_every_other_year_mets
-#&gt; $Pesticide_D_1_May_every_other_year_mets$win
-#&gt; FOCUS DUMMY D M1 M2
-#&gt; Cha 0.001 126.195 0.000
-#&gt; Ham 0.054 82.196 0.001
-#&gt; Kre 0.103 75.494 0.001
-#&gt;
-#&gt; </div></pre>
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- <li><a href="#arguments">Arguments</a></li>
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