Correct psm file in the example with metabolites

3 files changed, 76 insertions, 2 deletions

diff --git a/docs/index.html b/docs/index.html
index db22eb0..0c53fe9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -75,6 +75,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <h2 class="hasAnchor">
 <a href="#examples" class="anchor"> </a>Examples</h2>
 <p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://jranke.github.io/pfm/reference/plot.one_box.html">here</a>.</p>
+<p>Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown <a href="http://jranke.github.io/pfm/reference/PELMO_runs.html">here</a>.</p>
 </div>
 </div>
   </div>
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index 79aa89d..ab24341 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -73,7 +73,7 @@
     <p>Create a path of run directories as the PELMO GUI does</p>
     
 
-    <pre><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='no'>scenario</span>)</pre>
+    <pre><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <dl class="dl-horizontal">
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>