diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/PEC_soil.Rd | 3 | ||||
| -rw-r--r-- | man/PEC_sw_drainage_UK.Rd | 5 | ||||
| -rw-r--r-- | man/PEC_sw_drift.Rd | 26 | ||||
| -rw-r--r-- | man/PEC_sw_exposit_drainage.Rd | 20 | ||||
| -rw-r--r-- | man/PEC_sw_exposit_runoff.Rd | 14 | ||||
| -rw-r--r-- | man/PEC_sw_sed.Rd | 10 | ||||
| -rw-r--r-- | man/TOXSWA_cwa.Rd | 2 | ||||
| -rw-r--r-- | man/drift_percentages_rautmann.Rd | 18 | ||||
| -rw-r--r-- | man/max_twa.Rd | 4 | ||||
| -rw-r--r-- | man/one_box.Rd | 6 | ||||
| -rw-r--r-- | man/perc_runoff_exposit.Rd | 2 | ||||
| -rw-r--r-- | man/perc_runoff_reduction_exposit.Rd | 2 | ||||
| -rw-r--r-- | man/plot.one_box.Rd | 5 | ||||
| -rw-r--r-- | man/sawtooth.Rd | 2 | ||||
| -rw-r--r-- | man/twa.Rd | 2 |
15 files changed, 70 insertions, 51 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/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index 0923f10..0e8a953 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -4,7 +4,7 @@ \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 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/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/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..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} @@ -47,8 +47,9 @@ 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{ -\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} @@ -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} } |