10 files changed, 60 insertions, 41 deletions
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index 391e25b..ed4c3f3 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -84,7 +84,8 @@ as Kom here}
 
 \item{t_act}{Time series for actual concentrations}
 
-\item{scenarios}{If this is 'default', the DT50 will be used without correction
+\item{scenarios}{If this is 'default', a soil bulk density of 1.5 kg/L will
+be used. The DT50 will be used without correction
 and soil properties as specified in the REACH guidance (R.16, Table
 R.16-9) are used for porewater PEC calculations.  If this is "EFSA_2015",
 the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index f3d6169..6125c3c 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -35,10 +35,13 @@ The predicted concentration in surface water in µg/L
 }
 \description{
 This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
-published on the CRC website
+published on the CRC website. Degradation before the start of the drainage period is taken into account if
+\code{latest_application} is specified and the degradation parameters are given either as a \code{soil_DT50} or a \code{model}.
 }
 \examples{
 PEC_sw_drainage_UK(150, Koc = 100)
+PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550,
+  latest_application = "01 July", soil_DT50 = 200)
 }
 \references{
 HSE's Chemicals Regulation Division (CRD) Active substance
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index c576753..5f3049a 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -7,23 +7,24 @@
 PEC_sw_drift(
   rate,
   applications = 1,
-  water_depth = 30,
+  water_depth = as_units("30 cm"),
   drift_percentages = NULL,
   drift_data = c("JKI", "RF"),
   crop_group_JKI = c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh",
     "Weinbau spaet", "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen"),
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
     "fruit, early", "aerial"),
   distances = c(1, 5, 10, 20),
   formula = c("Rautmann", "FOCUS"),
-  water_width = 100,
+  water_width = as_units("100 cm"),
   side_angle = 90,
   rate_units = "g/ha",
   PEC_units = "µg/L"
 )
 }
 \arguments{
-\item{rate}{Application rate in units specified below}
+\item{rate}{Application rate in units specified below, or with units defined via the
+\code{units} package.}
 
 \item{applications}{Number of applications for selection of drift percentile}
 
@@ -38,9 +39,9 @@ either in the original form or integrated over the width of the water body, depe
 on the 'formula' argument.}
 
 \item{crop_group_JKI}{When using the 'JKI' drift data, one of the German names
-as used in \link{drift_parameters_focus}.}
+as used in \link{drift_data_JKI}. Will only be used if drift_data is 'JKI'.}
 
-\item{crop_group_focus}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
 
 \item{distances}{The distances in m for which to get PEC values}
 
@@ -53,7 +54,8 @@ calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance}
 \item{side_angle}{The angle of the side of the water relative to the bottom which
 is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees here.}
 
-\item{rate_units}{Defaults to g/ha}
+\item{rate_units}{Defaults to g/ha. For backwards compatibility, only used
+if the specified rate does not have \link[units:units]{units::units}].}
 
 \item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported}
 }
@@ -65,6 +67,10 @@ This is a basic, vectorised form of a simple calculation of a contaminant
 concentration in surface water based on complete, instantaneous mixing
 with input via spray drift.
 }
+\details{
+It is recommened to specify the arguments \code{rate}, \code{water_depth} and
+\code{water_width} using \link[units:units]{units::units} from the \code{units} package.
+}
 \examples{
 PEC_sw_drift(100)
 # Alternatively, we can use the formula for a single application to
@@ -75,13 +81,13 @@ PEC_sw_drift(100, drift_data = "RF")
 PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF")
 
 # or consider aerial application
-PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", 
-  crop_group_focus = "aerial")
+PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF",
+  crop_group_RF = "aerial")
 
 # Using custom drift percentages is also supported
 PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03))
 
-# The influence of assuming a 45° angle of the sides of the waterbody and the width of the 
+# The influence of assuming a 45° angle of the sides of the waterbody and the width of the
 # waterbody can be illustrated
 PEC_sw_drift(100)
 PEC_sw_drift(100, drift_data = "RF")
diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd
index c809e08..f0c6160 100644
--- a/man/PEC_sw_exposit_drainage.Rd
+++ b/man/PEC_sw_exposit_drainage.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/PEC_sw_exposit_runoff.R
+% Please edit documentation in R/PEC_sw_exposit.R
 \name{PEC_sw_exposit_drainage}
 \alias{PEC_sw_exposit_drainage}
 \title{Calculate PEC surface water due to drainage as in Exposit 3}
@@ -13,10 +13,10 @@ PEC_sw_exposit_drainage(
   interception = 0,
   Koc = NA,
   mobility = c(NA, "low", "high"),
-  DT50 = Inf,
-  t_drainage = 3,
-  V_ditch = 30,
-  V_drainage = c(spring = 10, autumn = 100),
+  DT50 = set_units(Inf, "d"),
+  t_drainage = set_units(3, "days"),
+  V_ditch = set_units(30, "m3"),
+  V_drainage = set_units(c(spring = 10, autumn = 100), "m3"),
   dilution = 2
 )
 }
@@ -44,10 +44,10 @@ autumn/winter/early spring.}
 \value{
 A list containing the following components
 \describe{
-\item{perc_runoff}{The runoff percentages for dissolved and bound substance}
-\item{runoff}{A matrix containing dissolved and bound input for the different distances}
-\item{PEC_sw_runoff}{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.}
+\item{perc_drainage_total}{Gesamtaustrag (total fraction of the residue drained)}
+\item{perc_peak}{Stoßbelastung (fraction drained at event)}
+\item{PEC_sw_drainage}{A matrix containing PEC values for the spring and autumn
+scenarios. If the rate was given in g/ha, the PECsw are in microg/L.}
 }
 }
 \description{
@@ -58,6 +58,8 @@ calculations, between compounds with low mobility (group 1) and compounds
 with modest to high mobility (groups 2, 3 and 4). In this implementation,
 the group is derived only from the Koc, if not given explicitly. For
 details, see the discussion of the function arguments below.
+It is recommened to specify the arguments \code{rate}, \code{Koc}, \code{DT50}, \code{t_drainage},
+\code{V_ditch} and \code{V_drainage} using \link[units:units]{units::units} from the \code{units} package.
 }
 \examples{
   PEC_sw_exposit_drainage(500, Koc = 150)
diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd
index fca5553..393ed29 100644
--- a/man/PEC_sw_exposit_runoff.Rd
+++ b/man/PEC_sw_exposit_runoff.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/PEC_sw_exposit_runoff.R
+% Please edit documentation in R/PEC_sw_exposit.R
 \name{PEC_sw_exposit_runoff}
 \alias{PEC_sw_exposit_runoff}
 \title{Calculate PEC surface water due to runoff and erosion as in Exposit 3}
@@ -12,11 +12,11 @@ PEC_sw_exposit_runoff(
   rate,
   interception = 0,
   Koc,
-  DT50 = Inf,
-  t_runoff = 3,
+  DT50 = set_units(Inf, "d"),
+  t_runoff = set_units(3, "days"),
   exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"),
-  V_ditch = 30,
-  V_event = 100,
+  V_ditch = set_units(30, "m3"),
+  V_event = set_units(100, "m3"),
   dilution = 2
 )
 }
@@ -56,6 +56,10 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic
 This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file,
 in the worksheet "Konzept Runoff".
 }
+\details{
+It is recommened to specify the arguments \code{rate}, \code{Koc}, \code{DT50}, \code{t_runoff}, \code{V_ditch} and \code{V_event}
+using \link[units:units]{units::units} from the \code{units} package.
+}
 \examples{
   PEC_sw_exposit_runoff(500, Koc = 150)
   PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = "3.01a")
diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd
index bc82ee3..0ebfd28 100644
--- a/man/PEC_sw_sed.Rd
+++ b/man/PEC_sw_sed.Rd
@@ -9,9 +9,9 @@ PEC_sw_sed(
   PEC_sw,
   percentage = 100,
   method = "percentage",
-  sediment_depth = 5,
-  water_depth = 30,
-  sediment_density = 1.3,
+  sediment_depth = set_units(5, "cm"),
+  water_depth = set_units(30, "cm"),
+  sediment_density = set_units(1.3, "kg/L"),
   PEC_sed_units = c("µg/kg", "mg/kg")
 )
 }
@@ -27,7 +27,7 @@ which the corresponding sediment concentration is to be estimated}
 
 \item{water_depth}{Depth of the water body in cm}
 
-\item{sediment_density}{The density of the sediment in L/kg (equivalent to
+\item{sediment_density}{The density of the sediment in kg/L (equivalent to
 g/cm3)}
 
 \item{PEC_sed_units}{The units of the estimated sediment PEC value}
@@ -40,6 +40,8 @@ The method 'percentage' is equivalent to what is used in the CRD spreadsheet
 PEC calculator
 }
 \examples{
+library(pfm)
+library(units)
 PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
 }
 \author{
diff --git a/man/drift_percentages_rautmann.Rd b/man/drift_percentages_rautmann.Rd
index 5fb2586..e2a50d1 100644
--- a/man/drift_percentages_rautmann.Rd
+++ b/man/drift_percentages_rautmann.Rd
@@ -7,7 +7,7 @@
 drift_percentages_rautmann(
   distances,
   applications = 1,
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
     "fruit, early", "aerial"),
   formula = c("Rautmann", "FOCUS"),
   widths = 1
@@ -18,7 +18,7 @@ drift_percentages_rautmann(
 
 \item{applications}{Number of applications for selection of drift percentile}
 
-\item{crop_group_focus}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
 
 \item{formula}{By default, the original Rautmann formula is used. If you
 specify "FOCUS", mean drift input over the width of the water body is
@@ -30,7 +30,7 @@ calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance}
 Calculate drift percentages based on Rautmann data
 }
 \examples{
-# Compare JKI data with Rautmann formula
+# Compare JKI data with Rautmann and FOCUS formulas for arable crops (default)
 # One application on field crops, for 1 m, 3 m and 5 m distance
 drift_data_JKI[[1]][as.character(c(1, 3, 5)), "Ackerbau"]
 drift_percentages_rautmann(c(1, 3, 5))
@@ -38,20 +38,20 @@ drift_percentages_rautmann(c(1, 3, 5), formula = "FOCUS")
 
 # One application to early or late fruit crops
 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau frueh"]
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early")
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early",
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early")
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early",
   formula = "FOCUS")
 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau spaet"]
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late")
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late",
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late")
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late",
   formula = "FOCUS")
 
 # We get a continuum if the waterbody covers the hinge distance
 # (11.4 m for 1 early app to fruit)
 x <- seq(3, 30, by = 0.1)
-d <- drift_percentages_rautmann(x, crop_group = "fruit, early", formula = "FOCUS")
+d <- drift_percentages_rautmann(x, crop_group_RF = "fruit, early", formula = "FOCUS")
 plot(x, d, type = "l",
-  xlab = "Distance of near edge [m]", 
+  xlab = "Distance of near edge [m]",
   ylab = "Mean drift percentage over waterbody width",
   main = "One application to fruit, early")
 abline(v = 11.4, lty = 2)
diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd
index 47ea586..e30ab73 100644
--- a/man/perc_runoff_exposit.Rd
+++ b/man/perc_runoff_exposit.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/PEC_sw_exposit_runoff.R
+% Please edit documentation in R/PEC_sw_exposit.R
 \docType{data}
 \name{perc_runoff_exposit}
 \alias{perc_runoff_exposit}
diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd
index 2fc32a6..4514a58 100644
--- a/man/perc_runoff_reduction_exposit.Rd
+++ b/man/perc_runoff_reduction_exposit.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/PEC_sw_exposit_runoff.R
+% Please edit documentation in R/PEC_sw_exposit.R
 \docType{data}
 \name{perc_runoff_reduction_exposit}
 \alias{perc_runoff_reduction_exposit}
diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd
index 35e7bf7..443be99 100644
--- a/man/plot.one_box.Rd
+++ b/man/plot.one_box.Rd
@@ -47,6 +47,7 @@ m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
 fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 pred_2 <- one_box(fit_2, ini = 1)
 pred_2_saw <- sawtooth(pred_2, 2, 7)
+plot(pred_2_saw)
 plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
 }
 \seealso{