10 files changed, 97 insertions, 33 deletions
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index 058e068..b641114 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/PEC_sw_drainage_UK.R
 \name{PEC_sw_drainage_UK}
 \alias{PEC_sw_drainage_UK}
+\alias{drainage_date_UK}
 \title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
 \usage{
 PEC_sw_drainage_UK(
@@ -13,43 +14,56 @@ PEC_sw_drainage_UK(
   model = NULL,
   model_parms = NULL
 )
+
+drainage_date_UK(application_date)
 }
 \arguments{
-\item{rate}{Application rate in g/ha}
+\item{rate}{Application rate in g/ha or with a compatible unit specified
+with the units package}
 
 \item{interception}{The fraction of the application rate that does not reach the soil}
 
-\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg}
+\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg or a unit specified
+with the units package}
 
 \item{latest_application}{Latest application date, formatted as e.g. "01 July"}
 
-\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used}
+\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used, in
+days or a time unit specified with the units package}
 
 \item{model}{The soil degradation model to be used. Either one of "FOMC",
 "DFOP", "HS", or "IORE", or an mkinmod object}
 
 \item{model_parms}{A named numeric vector containing the model parameters}
+
+\item{application_date}{Application date}
 }
 \value{
 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. Degradation before the start of the drainage period is taken into account if
+published on the CRC website. Degradation between the end (30 April) and the start (1 October) 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)
+drainage_date_UK("2023-07-10")
+drainage_date_UK("2020-12-01")
+drainage_date_UK(as.Date("2022-01-15"))
 }
 \references{
 HSE's Chemicals Regulation Division (CRD) Active substance
 PECsw calculations (for UK specific authorisation requests)
-\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm}
-accessed 2019-09-27
+\url{https://www.hse.gov.uk/pesticides/data-requirements-handbook/fate/pecsw-sed-via-drainflow.htm}
+accessed 2026-02-13
 
-Drainage PECs Version 1.0 (2015) Spreadsheet published at
-\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx}
-accessed 2019-09-27
+PECsw/sed spray drift and tier 1 drainflow calculator Version 2.1.1 (2025) Spreadsheet published at
+\url{https://www.hse.gov.uk/pesticides/assets/docs/PEC\%20sw-sed\%20(spraydrift).xlsx)}
+accessed 2026-02-13
 }
 \author{
 Johannes Ranke
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index 771687e..89919bb 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -10,10 +10,8 @@ PEC_sw_drift(
   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_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
-    "fruit, early", "aerial"),
+  crop_group_JKI = "Ackerbau",
+  crop_group_RF = "arable",
   distances = c(1, 5, 10, 20),
   formula = c("Rautmann", "FOCUS"),
   water_width = as_units("100 cm"),
@@ -31,7 +29,8 @@ PEC_sw_drift(
 \item{water_depth}{Depth of the water body in cm}
 
 \item{drift_percentages}{Percentage drift values for which to calculate PECsw.
-Overrides 'drift_data' and 'distances' if not NULL.}
+Overrides 'drift_data', 'distances', 'applications', crop group and
+formula arguments if not NULL.}
 
 \item{drift_data}{Source of drift percentage data. If 'JKI', the \link{drift_data_JKI}
 included in the package is used. If 'RF', the Rautmann drift data are calculated
@@ -39,9 +38,14 @@ 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}. Will only be used if drift_data is 'JKI'.}
+as used in \link{drift_data_JKI}. Will only be used if drift_data is 'JKI'. Available
+crop groups are "Ackerbau", "Obstbau frueh", "Obstbau spaet",
+"Weinbau frueh", "Weinbau spaet", "Hopfenbau", "Flaechenkulturen > 900 l/ha" and
+"Gleisanlagen".}
 
-\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{Crop group(s) as used in \link{drift_parameters_focus}, i.e.
+"arable", "hops", "vines, late", "vines, early", "fruit, late", "fruit, early"
+or "aerial".}
 
 \item{distances}{The distances in m for which to get PEC values}
 
@@ -60,7 +64,10 @@ 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}
 }
 \value{
-The predicted concentration in surface water
+A numeric vector with the predicted concentration in surface water.
+In some cases, the vector is named with distances or drift percentages, for
+backward compatibility with versions before the vectorisation of arguments
+other than 'distances' was introduced in v0.6.5.
 }
 \description{
 This is a basic, vectorised form of a simple calculation of a contaminant
@@ -70,6 +77,9 @@ 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.
+
+Since pfm version 0.6.5, the function is vectorised with respect to rates,
+applications, water depth, crop groups and distances
 }
 \examples{
 PEC_sw_drift(100)
@@ -94,6 +104,34 @@ PEC_sw_drift(100, drift_data = "RF")
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS")
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS", side_angle = 45)
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS", side_angle = 45, water_width = 200)
+
+# The function is vectorised with respect to rates, applications, water depth,
+# crop groups and distances
+PEC_sw_drift(
+  rate = rep(100, 6),
+  applications = c(1, 2, rep(1, 4)),
+  water_depth = c(30, 30, 30, 60, 30, 30),
+  crop_group_JKI = c(rep("Ackerbau", 4), rep("Obstbau frueh", 2)),
+  distances = c(rep(5, 4), 10, 5))
+
+# Try the same with the Rautmann formula
+PEC_sw_drift(
+  rate = rep(100, 6),
+  applications = c(1, 2, rep(1, 4)),
+  water_depth = c(30, 30, 30, 60, 30, 30),
+  drift_data = "RF",
+  crop_group_RF = c(rep("arable", 4), rep("fruit, early", 2)),
+  distances = c(rep(5, 4), 10, 5))
+
+# And with the FOCUS variant
+PEC_sw_drift(
+  rate = rep(100, 6),
+  applications = c(1, 2, rep(1, 4)),
+  water_depth = c(30, 30, 30, 60, 30, 30),
+  drift_data = "RF",
+  formula = "FOCUS",
+  crop_group_RF = c(rep("arable", 4), rep("fruit, early", 2)),
+  distances = c(rep(5, 4), 10, 5))
 }
 \seealso{
 \link{drift_parameters_focus}, \link{drift_percentages_rautmann}
diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd
index 393ed29..4988d1d 100644
--- a/man/PEC_sw_exposit_runoff.Rd
+++ b/man/PEC_sw_exposit_runoff.Rd
@@ -21,7 +21,8 @@ PEC_sw_exposit_runoff(
 )
 }
 \arguments{
-\item{rate}{The application rate in g/ha}
+\item{rate}{Application rate in g/ha or with a compatible unit specified
+with the units package}
 
 \item{interception}{The fraction intercepted by the crop}
 
@@ -48,7 +49,7 @@ 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
+\item{PEC_sw_runoff}{A dataframe 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.}
 }
 }
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 0923f10..126fed4 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -4,14 +4,14 @@
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
 \format{
-An \code{\link{R6Class}} generator object.
+An \link[R6:R6Class]{R6::R6Class} generator object.
 }
 \description{
 An R6 class for holding TOXSWA water concentration (cwa) data
 and some associated statistics.  like maximum moving window average
 concentrations, and dataframes holding the events exceeding specified
 thresholds.  Usually, an instance of this class will be generated
-by \code{\link{read.TOXSWA_cwa}}.
+by \link{read.TOXSWA_cwa}.
 }
 \examples{
 H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
diff --git a/man/drift_percentages_rautmann.Rd b/man/drift_percentages_rautmann.Rd
index e2a50d1..ff84854 100644
--- a/man/drift_percentages_rautmann.Rd
+++ b/man/drift_percentages_rautmann.Rd
@@ -7,8 +7,7 @@
 drift_percentages_rautmann(
   distances,
   applications = 1,
-  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
-    "fruit, early", "aerial"),
+  crop_group_RF = "arable",
   formula = c("Rautmann", "FOCUS"),
   widths = 1
 )
@@ -18,7 +17,9 @@ drift_percentages_rautmann(
 
 \item{applications}{Number of applications for selection of drift percentile}
 
-\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{Crop group(s) as used in \link{drift_parameters_focus}, i.e.
+"arable", "hops", "vines, late", "vines, early", "fruit, late", "fruit, early"
+or "aerial".}
 
 \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
@@ -36,6 +37,16 @@ drift_data_JKI[[1]][as.character(c(1, 3, 5)), "Ackerbau"]
 drift_percentages_rautmann(c(1, 3, 5))
 drift_percentages_rautmann(c(1, 3, 5), formula = "FOCUS")
 
+# Since pfm 0.6.5, the function can also take a vector of crop groups
+drift_percentages_rautmann(
+  distances = c(1, 5, 5),
+  crop_group_RF = c("fruit, early", "fruit, early", "fruit, late"))
+
+# Two applications, all else equal
+drift_data_JKI[[2]][as.character(c(1, 3, 5)), "Ackerbau"]
+drift_percentages_rautmann(c(1, 3, 5), applications = 2)
+drift_percentages_rautmann(c(1, 3, 5), formula = "FOCUS", app = 2)
+
 # 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_RF = "fruit, early")
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 43ad50e..2bba22f 100644
--- a/man/max_twa.Rd
+++ b/man/max_twa.Rd
@@ -7,7 +7,7 @@
 max_twa(x, window = 21)
 }
 \arguments{
-\item{x}{An object of type \code{\link{one_box}}}
+\item{x}{An object of type \link{one_box}}
 
 \item{window}{The size of the moving window}
 }
@@ -19,7 +19,7 @@ for finding the maximum. It is therefore recommended to check this using
 \code{max_twa}.
 }
 \details{
-The method working directly on fitted \code{\link{mkinfit}} objects uses the
+The method working directly on fitted \link[mkin:mkinfit]{mkin::mkinfit} objects uses the
 equations given in the PEC soil section of the FOCUS guidance and is restricted
 SFO, FOMC and DFOP models and to the parent compound
 }
diff --git a/man/one_box.Rd b/man/one_box.Rd
index a60aa39..83a9fe0 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -19,10 +19,10 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 \item{x}{When numeric, this is the half-life to be used for an exponential
 decline. When a character string specifying a parent decline model is given
 e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
-If x is an \code{\link{mkinfit}} object, the decline is calculated from this
+If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, the decline is calculated from this
 object.}
 
-\item{ini}{The initial amount. If x is an \code{\link{mkinfit}} object, and
+\item{ini}{The initial amount. If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, and
 ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 must be numeric. If it has length one, it is used for the parent and
 initial values of metabolites are zero, otherwise, it must give values for
@@ -37,7 +37,7 @@ all observed variables.}
 \item{parms}{A named numeric vector containing the model parameters}
 }
 \value{
-An object of class \code{one_box}, inheriting from \code{\link{ts}}.
+An object of class \code{one_box}, inheriting from \link{ts}.
 }
 \description{
 Create a time series of decline data
diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd
index 443be99..91fddf0 100644
--- a/man/plot.one_box.Rd
+++ b/man/plot.one_box.Rd
@@ -16,7 +16,7 @@
 )
 }
 \arguments{
-\item{x}{The object of type \code{\link{one_box}} to be plotted}
+\item{x}{The object of type \link{one_box} to be plotted}
 
 \item{xlim}{Limits for the x axis}
 
@@ -51,5 +51,5 @@ plot(pred_2_saw)
 plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
 }
 \seealso{
-\code{\link{sawtooth}}
+\link{sawtooth}
 }
diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd
index 0850ded..d85b161 100644
--- a/man/sawtooth.Rd
+++ b/man/sawtooth.Rd
@@ -12,7 +12,7 @@ sawtooth(
 )
 }
 \arguments{
-\item{x}{A \code{\link{one_box}} object}
+\item{x}{A \link{one_box} object}
 
 \item{n}{The number of applications. If \code{applications} is specified, \code{n} is ignored}
 
diff --git a/man/twa.Rd b/man/twa.Rd
index a3509cd..da66257 100644
--- a/man/twa.Rd
+++ b/man/twa.Rd
@@ -10,7 +10,7 @@ twa(x, window = 21)
 \method{twa}{one_box}(x, window = 21)
 }
 \arguments{
-\item{x}{An object of type \code{\link{one_box}}}
+\item{x}{An object of type \link{one_box}}
 
 \item{window}{The size of the moving window}
 }