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-rw-r--r--ChangeLog6
-rw-r--r--DESCRIPTION2
-rw-r--r--GNUmakefile2
-rw-r--r--R/PEC_sw_exposit_runoff.R16
-rw-r--r--_pkgdown.yml5
-rw-r--r--docs/reference/PEC_sw_exposit_runoff.html31
-rw-r--r--docs/reference/index.html26
-rw-r--r--docs/reference/one_box-2.pngbin15306 -> 15306 bytes
-rw-r--r--docs/reference/one_box-3.pngbin30098 -> 30090 bytes
-rw-r--r--docs/reference/perc_runoff_reduction_exposit.html18
-rw-r--r--docs/reference/plot.one_box-3.pngbin37317 -> 37322 bytes
-rw-r--r--docs/reference/sawtooth-2.pngbin37317 -> 37322 bytes
-rw-r--r--man/PEC_sw_exposit_runoff.Rd9
-rw-r--r--man/perc_runoff_reduction_exposit.Rd3
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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

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