Add Exposit version 3.01a2 for runoff calculations

At the request of Muris Korkaric (Agroscope). This is for 3 m buffer
only and provides consistency with earlier calculations

14 files changed, 91 insertions, 27 deletions

diff --git a/ChangeLog b/ChangeLog
index bd16f8c..e2942c0 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+commit 7b11b5d0da29447df026002af3ae5283510fdae9
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-04-29 13:03:00 +0200
+
+    Additional runoff data used by Agroscope
+
 commit 67cd9e04caaf18a40231262c9033fb24e8bb2a66
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2019-04-26 13:45:44 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 4747803..5162c06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.5.5
-Date: 2019-04-27
+Date: 2019-05-14
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
diff --git a/GNUmakefile b/GNUmakefile
index c8803ab..76d369e 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -67,7 +67,7 @@ quickcheck: build
 
 check: build
 	@echo "Running CRAN check..."
-	"$(R_HOME)/bin/R" CMD check --as-cran $(TGZ)
+	_R_CHECK_CRAN_INCOMING_REMOTE_=false "$(R_HOME)/bin/R" CMD check --as-cran $(TGZ)
 	@echo "DONE."
 
 install: build
diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R
index 22316bc..d4b2c90 100644
--- a/R/PEC_sw_exposit_runoff.R
+++ b/R/PEC_sw_exposit_runoff.R
@@ -42,7 +42,8 @@ rownames(perc_runoff_exposit) <- Koc_classes
 #' @source Excel 3.02 spreadsheet available from
 #'   \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
 #'   
-#'   Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published)
+#'   Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published).
+#'   The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.
 #' @export
 #' @examples
 #' print(perc_runoff_reduction_exposit)
@@ -53,9 +54,12 @@ perc_runoff_reduction_exposit <- list(
     row.names = c("No buffer", paste(c(5, 10, 20), "m"))),
    "3.01a" = data.frame(
     dissolved = c(0, 25, 40, 45, 60, 80),
-    bound = c(0, 7.1, 13.3, 15.9, 25.7, 48),
-    #bound = c(0, 30, 40, 55, 85, 95),
+    bound = c(0, 30, 40, 55, 85, 95),
     row.names = c("No buffer", paste(c(3, 5, 6, 10, 20), "m"))),
+   "3.01a2" = data.frame(
+    dissolved = c(0, 25),
+    bound = c(0, 25),
+    row.names = c("No buffer", paste(c(3), "m"))),
   "2.0" = data.frame(
     dissolved = c(0, 97.5),
     bound = c(0, 97.5),
@@ -74,7 +78,9 @@ perc_runoff_reduction_exposit <- list(
 #' @param t_runoff The time between application and the runoff event, where degradation occurs, in days
 #' @param exposit_reduction_version The version of the reduction factors to be used. "3.02" is the current
 #'   version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer
-#'   zones used in Switzerland.
+#'   zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations
+#'   performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved
+#'   and the bound fraction.
 #' @param V_ditch The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3
 #' @param V_event The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha
 #' @param dilution The dilution factor
@@ -93,7 +99,7 @@ perc_runoff_reduction_exposit <- list(
 #'   PEC_sw_exposit_runoff(500, Koc = 150)
 #'   PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = "3.01a")
 PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_runoff = 3,
-  exposit_reduction_version = c("3.02", "3.01a", "2.0"),
+  exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"),
   V_ditch = 30, V_event = 100, dilution = 2)
 {
   k_deg <- log(2)/DT50
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 93da47e..798834b 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -32,12 +32,13 @@ reference:
       - drift_data_JKI
       - PEC_sw_drainage_UK
       - PEC_sw_sed
-      - chent_focus_sw
       - PEC_sw_focus
+      - chent_focus_sw
       - FOCUS_Step_12_scenarios
+      - PEC_sw_exposit_drainage
+      - PEC_sw_exposit_runoff
       - perc_runoff_exposit
       - perc_runoff_reduction_exposit
-      - PEC_sw_exposit_runoff
       - TOXSWA_cwa
       - read.TOXSWA_cwa
       - plot.TOXSWA_cwa
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 4d1b5de..742c233 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -113,8 +113,8 @@ in the worksheet "Konzept Runoff".</p>
     </div>
 
     <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>,
-  <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"2.0"</span>),
-  <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
+  <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>,
+  <span class='st'>"3.01a2"</span>, <span class='st'>"2.0"</span>), <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -141,7 +141,11 @@ in the worksheet "Konzept Runoff".</p>
     </tr>
     <tr>
       <th>exposit_reduction_version</th>
-      <td><p>The version of the reduction factors to be used</p></td>
+      <td><p>The version of the reduction factors to be used. "3.02" is the current
+version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer
+zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations
+performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved
+and the bound fraction.</p></td>
     </tr>
     <tr>
       <th>V_ditch</th>
@@ -195,6 +199,27 @@ in the worksheet "Konzept Runoff".</p>
 #&gt; 5 m        4.133333 0.016666667 4.150000
 #&gt; 10 m       3.542857 0.005357143 3.548214
 #&gt; 20 m       2.480000 0.002500000 2.482500
+#&gt; </div><div class='input'>  <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>600</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>195</span>, <span class='kw'>exposit</span> <span class='kw'>=</span> <span class='st'>"3.01a"</span>)</div><div class='output co'>#&gt; $perc_runoff
+#&gt; dissolved     bound 
+#&gt;     0.037     0.159 
+#&gt; 
+#&gt; $runoff
+#&gt;            dissolved      bound      total
+#&gt; No buffer 0.21964521 0.94388078 1.16352600
+#&gt; 3 m       0.16473391 0.66071655 0.82545046
+#&gt; 5 m       0.13178713 0.56632847 0.69811560
+#&gt; 6 m       0.12080487 0.42474635 0.54555122
+#&gt; 10 m      0.08785809 0.14158212 0.22944020
+#&gt; 20 m      0.04392904 0.04719404 0.09112308
+#&gt; 
+#&gt; $PEC_sw_runoff
+#&gt;           dissolved     bound     total
+#&gt; No buffer 0.8447893 3.6303107 4.4751000
+#&gt; 3 m       0.7844472 3.1462693 3.9307165
+#&gt; 5 m       0.7321507 3.1462693 3.8784200
+#&gt; 6 m       0.7106169 2.4985080 3.2091248
+#&gt; 10 m      0.6275578 1.0113008 1.6388586
+#&gt; 20 m      0.4392904 0.4719404 0.9112308
 #&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index cb2d963..21b75c7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -257,15 +257,15 @@ water concentrations</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p>
+          <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p>
         </td>
-        <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td>
+        <td><p>Calculate PEC surface water at FOCUS Step 1</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p>
+          <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p>
         </td>
-        <td><p>Calculate PEC surface water at FOCUS Step 1</p></td>
+        <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td>
       </tr><tr>
         
         <td>
@@ -275,21 +275,27 @@ water concentrations</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p>
+          <p><code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p>
         </td>
-        <td><p>Runoff loss percentages as used in Exposit 3</p></td>
+        <td><p>Calculate PEC surface water due to drainage as in Exposit 3</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p>
+          <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p>
         </td>
-        <td><p>Runoff reduction percentages as used in Exposit</p></td>
+        <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p>
+          <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p>
         </td>
-        <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td>
+        <td><p>Runoff loss percentages as used in Exposit 3</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p>
+        </td>
+        <td><p>Runoff reduction percentages as used in Exposit</p></td>
       </tr><tr>
         
         <td>
diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png
index 0da7911..eb60bd6 100644
--- a/docs/reference/one_box-2.png
+++ b/docs/reference/one_box-2.png
diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png
index c770252..fcb308b 100644
--- a/docs/reference/one_box-3.png
+++ b/docs/reference/one_box-3.png
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index 2800d7e..314e793 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -125,7 +125,9 @@ from which the values were taken.</p><dl class='dl-horizontal'>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Excel 3.02 spreadsheet available from
-  <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p>
+  <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p>  
+<p>Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published).
+  The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -136,6 +138,20 @@ from which the values were taken.</p><dl class='dl-horizontal'>
 #&gt; 10 m             60    85
 #&gt; 20 m             80    95
 #&gt; 
+#&gt; $`3.01a`
+#&gt;           dissolved bound
+#&gt; No buffer         0     0
+#&gt; 3 m              25    30
+#&gt; 5 m              40    40
+#&gt; 6 m              45    55
+#&gt; 10 m             60    85
+#&gt; 20 m             80    95
+#&gt; 
+#&gt; $`3.01a2`
+#&gt;           dissolved bound
+#&gt; No buffer         0     0
+#&gt; 3 m              25    25
+#&gt; 
 #&gt; $`2.0`
 #&gt;           dissolved bound
 #&gt; No buffer       0.0   0.0
diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png
index 9767472..b2c339b 100644
--- a/docs/reference/plot.one_box-3.png
+++ b/docs/reference/plot.one_box-3.png
diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png
index 9767472..b2c339b 100644
--- a/docs/reference/sawtooth-2.png
+++ b/docs/reference/sawtooth-2.png
diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd
index 13fae38..c73270b 100644
--- a/man/PEC_sw_exposit_runoff.Rd
+++ b/man/PEC_sw_exposit_runoff.Rd
@@ -9,8 +9,8 @@ Excel 3.02 spreadsheet available from
 }
 \usage{
 PEC_sw_exposit_runoff(rate, interception = 0, Koc, DT50 = Inf,
-  t_runoff = 3, exposit_reduction_version = c("3.02", "3.01a", "2.0"),
-  V_ditch = 30, V_event = 100, dilution = 2)
+  t_runoff = 3, exposit_reduction_version = c("3.02", "3.01a",
+  "3.01a2", "2.0"), V_ditch = 30, V_event = 100, dilution = 2)
 }
 \arguments{
 \item{rate}{The application rate in g/ha}
@@ -25,7 +25,9 @@ PEC_sw_exposit_runoff(rate, interception = 0, Koc, DT50 = Inf,
 
 \item{exposit_reduction_version}{The version of the reduction factors to be used. "3.02" is the current
 version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer
-zones used in Switzerland.}
+zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations
+performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved
+and the bound fraction.}
 
 \item{V_ditch}{The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3}
 
@@ -48,6 +50,7 @@ in the worksheet "Konzept Runoff".
 }
 \examples{
   PEC_sw_exposit_runoff(500, Koc = 150)
+  PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = "3.01a")
 }
 \seealso{
 \code{\link{perc_runoff_exposit}} for runoff loss percentages and \code{\link{perc_runoff_reduction_exposit}} for runoff reduction percentages used
diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd
index 7cb8f23..016f9dd 100644
--- a/man/perc_runoff_reduction_exposit.Rd
+++ b/man/perc_runoff_reduction_exposit.Rd
@@ -16,7 +16,8 @@ from which the values were taken.
 Excel 3.02 spreadsheet available from
   \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
   
-  Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published)
+  Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published).
+  The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.
 }
 \usage{
 perc_runoff_reduction_exposit