Correction of return value documentation for PEC_sw_exposit_runoff

Rebuild pkgdown documentation

12 files changed, 40 insertions, 24 deletions

diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 378c4e2..5539dc6 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -121,9 +121,10 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>A list containing the following components</p><dl class='dl-horizontal'>
-    <dt>Input</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd>
-    <dt>PEC_sw_runoo</dt><dd><p>A matrix containing PEC values for dissolved and bound substance
-      for the different distances. If the rate was given in g/ha, the PECsw are in /L.</p></dd>
+    <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd>
+    <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd>
+    <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance
+      for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd>
   </dl>
 
     
@@ -133,13 +134,11 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='fl'>150</span>)</div><div class='output co'>#&gt; $Rate
-#&gt; [1] 500
+    <pre class="examples"><div class='input'>  <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='fl'>150</span>)</div><div class='output co'>#&gt; $perc_runoff
+#&gt; dissolved     bound 
+#&gt;     0.248     0.001 
 #&gt; 
-#&gt; $Koc
-#&gt; [1] 150
-#&gt; 
-#&gt; $Input
+#&gt; $runoff
 #&gt;           dissolved   bound   total
 #&gt; No buffer     1.240 0.00500 1.24500
 #&gt; 5 m           0.744 0.00300 0.74700
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 9f6b7e8..f06c0fe 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;     218.896       1.000      55.247 </div><div class='input'>
+#&gt;     219.036       1.004      56.622 </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/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 908f233..f67df04 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -92,7 +92,7 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
     <dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd>
     <dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd>
     <dt><code>windows</code></dt><dd><p>Matrix of maximum time weighted average concentrations (TWAC_max)
-and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) 
+and areas under the curve in /day * h (AUC_max_h) or /day * d (AUC_max_d)
 for the requested moving window sizes in days.</p></dd>
 </dl>
     
@@ -101,8 +101,8 @@ for the requested moving window sizes in days.</p></dd>
     
     <dl class='dl-horizontal'>
   <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value
-        in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
-        adsorbed to suspended matter will be used. The resulting dataframe is stored in the 
+        in /L. If <code>total = TRUE</code>, the total concentration including the amount
+        adsorbed to suspended matter will be used. The resulting dataframe is stored in the
         <code>events</code> field of the object.</p></dd>
   <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above.
         Again, if <code>total = TRUE</code>, the total concentration including the amount
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index d951a9e..59dd40d 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -102,9 +102,9 @@ from which the values were taken.</p><dl class='dl-horizontal'>
 #&gt; 20 m             80    95
 #&gt; 
 #&gt; $`2.0`
-#&gt;   dissolved bound
-#&gt; 1       0.0   0.0
-#&gt; 2      97.5  97.5
+#&gt;           dissolved bound
+#&gt; No buffer       0.0   0.0
+#&gt; 20 m           97.5  97.5
 #&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
index 62a2df9..786f7f0 100644
--- a/docs/reference/pesticide.txt
+++ b/docs/reference/pesticide.txt
@@ -11,3 +11,5 @@ Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Du
 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
 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
+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
diff --git a/docs/reference/plot.TOXSWA_cwa-10.png b/docs/reference/plot.TOXSWA_cwa-10.png
new file mode 100644
index 0000000..4e5eae3
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-10.png
diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png
index 01737fa..b36bf11 100644
--- a/docs/reference/plot.TOXSWA_cwa-2.png
+++ b/docs/reference/plot.TOXSWA_cwa-2.png
diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png
new file mode 100644
index 0000000..cb1189b
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-4.png
diff --git a/docs/reference/plot.TOXSWA_cwa-6.png b/docs/reference/plot.TOXSWA_cwa-6.png
new file mode 100644
index 0000000..c21eacc
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-6.png
diff --git a/docs/reference/plot.TOXSWA_cwa-8.png b/docs/reference/plot.TOXSWA_cwa-8.png
new file mode 100644
index 0000000..04e09d6
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-8.png
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index 5375673..f2088f2 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -79,7 +79,8 @@ segment of a TOXSWA surface water body.</p>
     <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>,
   <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre>
+  <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>,
+  <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
@@ -102,6 +103,17 @@ the time is given in days relative to the first of January in the first year.</p
       <td><p>Should we add to an existing plot?</p></td>
     </tr>
     <tr>
+      <th>threshold_factor</th>
+      <td><p>The factor by which the data have to be lower than the maximum
+in order to get thinned for plotting (see next argument).</p></td>
+    </tr>
+    <tr>
+      <th>thin_low</th>
+      <td><p>If an integer greater than 1, the data close to zero (smaller than
+1/threshold_factor of the maximum) in the series will be thinned by this factor
+in order to decrease the amount of data that is included in the plots</p></td>
+    </tr>
+    <tr>
       <th>total</th>
       <td><p>Should the total concentration in water be plotted, including substance sorbed
 to suspended matter?</p></td>
@@ -119,10 +131,13 @@ to suspended matter?</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span>  <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>,
-                                 <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
-                                 <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
-                                             <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
-<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></pre>
+  <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
+  <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><img src='plot.TOXSWA_cwa-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><img src='plot.TOXSWA_cwa-6.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><img src='plot.TOXSWA_cwa-8.png' alt='' width='540' height='400' /><div class='input'>
+<span class='no'>H_sw_R1_stream</span>  <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
+  <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
+  <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><img src='plot.TOXSWA_cwa-10.png' alt='' width='540' height='400' /></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index 30e29cd..25e7dd7 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -101,7 +101,7 @@ out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</p></td>
     </tr>
     <tr>
       <th>segment</th>
-      <td><p>The segment for which the data should be read. Either "last", or 
+      <td><p>The segment for which the data should be read. Either "last", or
 the segment number.</p></td>
     </tr>
     <tr>
@@ -112,7 +112,7 @@ of interested can be selected by its code name.</p></td>
     </tr>
     <tr>
       <th>total</th>
-      <td><p>Set this to TRUE in order to read total concentrations as well. This is 
+      <td><p>Set this to TRUE in order to read total concentrations as well. This is
 only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
 files. For .cwa files, the total concentration is always read as well.</p></td>
     </tr>
@@ -123,7 +123,7 @@ maximum time weighted average concentrations and areas under the curve.</p></td>
     </tr>
     <tr>
       <th>thresholds</th>
-      <td><p>Numeric vector of threshold concentrations in µg/L for
+      <td><p>Numeric vector of threshold concentrations in /L for
 generating event statistics.</p></td>
     </tr>
     </table>