New Option for Step 1, fix example, update docs

Also add the reference file for testing Step12 input file generation

5 files changed, 81 insertions, 15 deletions

diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 7331d42..50651ae 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Calculate FOCUS Step 1 PEC surface water — PEC_sw_focus • pfm</title>
+<title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -68,19 +68,25 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Calculate FOCUS Step 1 PEC surface water</h1>
+    <h1>Calculate PEC surface water at FOCUS Step 1</h1>
     </div>
 
     
-    <p>This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator
-version 3.2, authored by Michael Klein. Note that results for multiple
+    <p>This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+authored by Michael Klein, in R. Note that results for multiple
 applications should be compared to the corresponding results for a
 single application. At current, this is not done automatically in
-this implementation.</p>
+this implementation. Only Step 1 PECs are calculated. However,
+input files are generated that are suitable as input also for Step 2
+to be used with the FOCUS calculator.</p>
     
 
-    <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>)</pre>
+    <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>,
+  <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
+  <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>,
+  <span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
@@ -104,6 +110,10 @@ applications are given explicitly</p></td>
       <td><p>The application interval</p></td>
     </tr>
     <tr>
+      <th>comment</th>
+      <td><p>A comment for the input file</p></td>
+    </tr>
+    <tr>
       <th>met</th>
       <td><p>A list containing metabolite specific parameters.  e.g.
 conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>.  If not NULL,
@@ -127,6 +137,42 @@ parent or a metabolite</p></td>
       <td><p>The name of the scenario. Must be one of the scenario
 names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td>
     </tr>
+    <tr>
+      <th>region</th>
+      <td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only
+Step 1 PECsw are calculated</p></td>
+    </tr>
+    <tr>
+      <th>season</th>
+      <td><p>'of' for October to February, 'mm' for March to May, and 'js'
+for June to September. If NA, only step 1 PECsw are calculated</p></td>
+    </tr>
+    <tr>
+      <th>interception</th>
+      <td><p>One of 'no interception' (default), 'minimal crop cover',
+'average crop cover' or 'full canopy'</p></td>
+    </tr>
+    <tr>
+      <th>met_form_water</th>
+      <td><p>Should the metabolite formation in water be taken into
+account? This can be switched off to check the influence and to compare
+with previous versions of the Steps 12 calculator</p></td>
+    </tr>
+    <tr>
+      <th>txt_file</th>
+      <td><p>the name, and potentially the full path to the
+Steps.12 input text file to which the specification of the run(s)
+should be written</p></td>
+    </tr>
+    <tr>
+      <th>overwrite</th>
+      <td><p>Should an existing file a the location specified in
+<code>txt_file</code> be overwritten?</p></td>
+    </tr>
+    <tr>
+      <th>append</th>
+      <td><p>Should the input text file be appended?</p></td>
+    </tr>
     </table>
     
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
@@ -151,7 +197,7 @@ names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenar
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># Parent only</span>
-<span class='no'>dummy_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>)
+<span class='no'>dummy_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>)
 <span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>)</div><div class='output co'>#&gt; $f_drift
 #&gt; [1] 0
 #&gt; 
@@ -198,8 +244,9 @@ names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenar
 #&gt; [1] 2362.075
 #&gt; </div><div class='input'>
 <span class='co'># Metabolite</span>
-<span class='no'>new_dummy</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)
-<span class='no'>M1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>new_dummy</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)
+<span class='no'>M1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>,
+  <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
 <span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#&gt; $f_drift
 #&gt; [1] 0.02759
 #&gt; 
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 25afcf0..f2df73a 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -190,7 +190,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
 #&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;     218.736       0.940      54.948 </div><div class='input'>
+#&gt;     218.452       0.788      55.054 </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>)))
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index bd3d084..8e95618 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -75,13 +75,17 @@
     <p>Create a chemical compound object for FOCUS Step 1 calculations</p>
     
 
-    <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-  <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+    <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</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>name</th>
+      <td><p>Length one character vector containing the name</p></td>
+    </tr>
+    <tr>
       <th>Koc</th>
       <td><p>Partition coefficient between organic carbon and water
 in L/kg.</p></td>
@@ -91,12 +95,24 @@ in L/kg.</p></td>
       <td><p>Half-life in water/sediment systems in days</p></td>
     </tr>
     <tr>
+      <th>DT50_soil</th>
+      <td><p>Half-life in soil in days</p></td>
+    </tr>
+    <tr>
+      <th>DT50_water</th>
+      <td><p>Half-life in water in days (Step 2)</p></td>
+    </tr>
+    <tr>
+      <th>DT50_sediment</th>
+      <td><p>Half-life in sediment in days (Step 2)</p></td>
+    </tr>
+    <tr>
       <th>cwsat</th>
       <td><p>Water solubility in mg/L</p></td>
     </tr>
     <tr>
       <th>mw</th>
-      <td><p>Molar weight in g/mol</p></td>
+      <td><p>Molar weight in g/mol.</p></td>
     </tr>
     <tr>
       <th>max_soil</th>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a6ae657..9973635 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -191,7 +191,7 @@ published by the JKI</p></td>
           <td>
             <p><code><a href="PEC_sw_focus.html">PEC_sw_focus</a></code> </p>
           </td>
-          <td><p>Calculate FOCUS Step 1 PEC surface water</p></td>
+          <td><p>Calculate PEC surface water at FOCUS Step 1</p></td>
         </tr><tr>
           <!--  -->
           <td>
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
new file mode 100644
index 0000000..e4c6dac
--- /dev/null
+++ b/docs/reference/pesticide.txt
@@ -0,0 +1,3 @@
+Active Substance	Compound	Comment	Mol mass a.i.	Mol mass met.	Water solubility	KOC assessed compound	KOC parent compound	DT50	Max. in Water	Max. in Soil asessed compound	App. Rate	Number of App.	Time between app.	App. Type	DT50 soil parent compound	DT50 soil	DT50 water	DT50 sediment	Region / Season	Interception class
+Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA	Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA		  -99.00	  -99.00	 6000.00	  344.80	0.00E+00	    6.00	0.00E+00	0.00E+00	 3000.00	    1.00	0.00E+00	0.00E+00	    1.00	    2.00	    3.00	    4.00	    5.00	    6.00	    7.00	    8.00	    9.00	   10.00	   11.00	   12.00	   13.00	   14.00	   15.00	   16.00	   17.00	   18.00	   19.00	   20.00	   21.00	   22.00	   23.00	   24.00	   25.00	   26.00	   27.00	   28.00	0.00E+00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00