From 36036b5901223591e7e21e8b73d8cd1fb034f4cb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 16 May 2017 15:43:50 +0200 Subject: Finish the Step 1 calculator including tests Some cleaning up. PELMO facilities do not currently work at my end, as I have no working wine installation on this computer --- R/PEC_sw_focus.R | 122 +++++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 97 insertions(+), 25 deletions(-) (limited to 'R/PEC_sw_focus.R') diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R index 5f3b3d2..21ed514 100644 --- a/R/PEC_sw_focus.R +++ b/R/PEC_sw_focus.R @@ -1,37 +1,75 @@ #' Calculate FOCUS Step 1 PEC surface water #' -#' This is an attempt to reimplement the FOCUS Step 1 and 2 calculator authored -#' by Michael Klein. The Step 1 and 2 scenario assumes an area ratio of 10:1 -#' between field and waterbody, and a water depth of 30 cm. -#' I did not (yet) implement the TWA formulas for times later than day 1, as I -#' did not understand them right away. -#' Also, Step 2 is not implemented (yet). +#' This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator +#' version 3.2, authored by Michael Klein. Note that results for multiple +#' applications should be compared to the corresponding results for a +#' single application. At current, this is not done automatically in +#' this implementation. #' +#' @importFrom utils read.table +#' @references FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). +#' FOrum for the Co-ordination of pesticde fate models and their USe. +#' http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf +#' @references Website of the Steps 1 and 2 calculator at the Joint Research +#' Center of the European Union: +#' http://esdac.jrc.ec.europa.eu/projects/stepsonetwo +#' @note The formulas for input to the waterbody via runoff/drainage of the +#' parent and subsequent formation of the metabolite in water is not +#' documented in the model description coming with the calculator +#' @note Step 2 is not implemented #' @export #' @param parent A list containing substance specific parameters #' @param rate The application rate in g/ha. Overriden when #' applications are given explicitly #' @param n The number of applications #' @param i The application interval -#' @param applications A dataframe containing times and amounts of each application -#' @param step At the moment, only Step 1 is implemented +#' @param met A list containing metabolite specific parameters. If not NULL, +#' the PEC is calculated for this compound, not the parent. +#' @param f_drift The fraction of the application rate reaching the waterbody +#' via drift. If NA, this is derived from the scenario name and the number +#' of applications via the drift data defined by the +#' \code{\link{FOCUS_Step_12_scenarios}} +#' @param f_rd The fraction of the amount applied reaching the waterbody via +#' runoff/drainage. At Step 1, it is assumed to be 10%, be it the +#' parent or a metabolite +#' @param scenario The name of the scenario. Must be one of the scenario +#' names given in \code{\link{FOCUS_Step_12_scenarios}} #' @examples +#' # Parent only #' dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8) #' PEC_sw_focus(dummy_1, 3000, f_drift = 0) +#' +#' # Metabolite +#' new_dummy <- chent_focus_sw(mw = 250, Koc = 100) +#' M1 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) +#' PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1) PEC_sw_focus <- function(parent, rate, n = 1, i = NA, - applications = data.frame(time = seq(0, 0 + n * i, length.out = n), - amount = rate), met = NULL, - step = 1, - f_drift = 0.02759, f_rd = 0.1) + f_drift = NA, f_rd = 0.1, + scenario = FOCUS_Step_12_scenarios$names) { + if (n > 1 & is.na(i)) stop("Please specify the interval i if n > 1") + + if (is.na(f_drift)) { + scenario = match.arg(scenario) + f_drift = FOCUS_Step_12_scenarios$drift[scenario, "1"] / 100 + # For Step 2 we would/will select the reduced percentiles for multiple apps: + # if (n <= 8) { + # f_drift = FOCUS_Step_12_scenarios$drift[scenario, as.character(n)] / 100 + # } else { + # f_drift = FOCUS_Step_12_scenarios$drift[scenario, ">8"] / 100 + # } + } + if (is.null(met)) { + cwsat = parent$cwsat mw_ratio = 1 max_soil = 1 max_ws = 1 Koc = parent$Koc DT50_ws = parent$DT50_ws } else { + cwsat = met$cwsat mw_ratio = met$mw / parent$mw max_soil = met$max_soil max_ws = met$max_ws @@ -41,17 +79,35 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, # Rates for a single application eq_rate_drift_s = mw_ratio * max_ws * rate + # Parent only, or metabolite formed in soil: eq_rate_rd_s = mw_ratio * max_soil * rate + # Metabolite formed in water (this part is not documented in the Help files + # of the Steps 1/2 calculator): + if (!is.null(met)) { + eq_rate_rd_parent_s = mw_ratio * max_ws * rate + eq_rate_rd_s_tot = eq_rate_rd_s + eq_rate_rd_parent_s + } else { + eq_rate_rd_parent_s = NA + eq_rate_rd_s_tot = eq_rate_rd_s + } # Drift input input_drift_s = f_drift * eq_rate_drift_s / 10 # mg/m2 - input_drift = n * input_drift_s # Runoff/drainage input ratio_field_wb = 10 # 10 m2 of field for each m2 of the waterbody - input_rd_s = f_rd * eq_rate_rd_s * ratio_field_wb / 10 + input_rd_s = f_rd * eq_rate_rd_s_tot * ratio_field_wb / 10 input_rd = n * input_rd_s + # No accumulation between multiple applications if 3 * DT50 < i + if (n > 1 && (3 * DT50_ws < i)) { + input_drift = input_drift_s + input_rd = input_rd_s + } else { + input_drift = n * input_drift_s + input_rd = n * input_rd_s + } + # Fraction of compound entering the water phase via runoff/drainage depth_sw = 0.3 # m depth_sed = 0.05 # m @@ -85,25 +141,41 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, PEC["1", "TWAECsw"] = (PEC_sw_0 + PEC["1", "PECsw"]) / 2 PEC["1", "TWAECsed"] = (PEC_sed_0 + PEC["1", "PECsed"]) / 2 - list(eq_rate_drift_s = eq_rate_drift_s, - eq_rate_rd_s = eq_rate_rd_s, - input_drift_s = input_drift_s, - input_rd_s = input_rd_s, - f_rd_sw = f_rd_sw, f_rd_sed = f_rd_sed, - PEC = PEC) + # Check if PEC_sw_max is above water solubility + PEC_sw_max = max(PEC[, "PECsw"]) + if (PEC_sw_max > 1000 * cwsat) { + warning("The maximum PEC surface water exceeds the water solubility") + } + + PEC_sed_max = max(PEC[, "PECsed"]) + + list(f_drift = f_drift, + eq_rate_drift_s = eq_rate_drift_s, + eq_rate_rd_s = eq_rate_rd_s, + eq_rate_rd_parent_s = eq_rate_rd_parent_s, + input_drift_s = input_drift_s, + input_rd_s = input_rd_s, + f_rd_sw = f_rd_sw, f_rd_sed = f_rd_sed, + PEC = PEC, + PEC_sw_max = PEC_sw_max, + PEC_sed_max = PEC_sed_max + ) } -#' Create an chemical compound object for FOCUS Step 1 and 2 calculations +#' Create a chemical compound object for FOCUS Step 1 calculations #' #' @export #' @param cwsat Water solubility in mg/L #' @param DT50_ws Half-life in water/sediment systems in days #' @param Koc Partition coefficient between organic carbon and water #' in L/kg. +#' @param mw Molar weight in g/mol +#' @param max_soil Maximum observed fraction (dimensionless) in soil +#' @param max_ws Maximum observed fraction (dimensionless) in water/sediment +#' systems #' @return A list with the substance specific properties -chent_focus_sw <- function(Koc, DT50_ws, cwsat = 1000) +chent_focus_sw <- function(Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1) { - list(Koc = Koc, DT50_ws = DT50_ws, cwsat = cwsat) + list(Koc = Koc, DT50_ws = DT50_ws, cwsat = cwsat, + mw = mw, max_soil = max_soil, max_ws = max_ws) } - - -- cgit v1.2.1