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authorJohannes Ranke <jranke@uni-bremen.de>2017-01-30 18:04:53 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-30 18:04:53 +0100
commit03bda75d343402dad99df2aad55611e11279b833 (patch)
tree5801b2facfa7c731ad35b7378d6b2b72dee66d5c /docs/reference/PELMO_runs.html
parent39d202b0a0f833c756bc98fb4961483de1b15353 (diff)
Correct psm file in the example with metabolites
Diffstat (limited to 'docs/reference/PELMO_runs.html')
-rw-r--r--docs/reference/PELMO_runs.html75
1 files changed, 74 insertions, 1 deletions
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 03b7b7b..e299b7c 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -112,20 +112,93 @@ as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012<
<dd>Should an existing run directories be overwritten</dd>
</dl>
+ <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://jranke.github.io/PELMO.installeR'>https://jranke.github.io/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'>6</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; 231.892 0.496 57.056 </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>
</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>
- </ul>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
</div>
</div>

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