diff options
| -rw-r--r-- | ChangeLog | 24 | ||||
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/PEC_sw_focus.R | 161 | ||||
| -rw-r--r-- | build.log | 3 | ||||
| -rw-r--r-- | inst/testdata/Steps_12_pesticide.txt | 12 | ||||
| -rw-r--r-- | man/PEC_sw_focus.Rd | 33 | ||||
| -rw-r--r-- | man/chent_focus_sw.Rd | 14 | ||||
| -rw-r--r-- | test.log | 2 | ||||
| -rw-r--r-- | tests/testthat/test_step_1.R | 172 |
9 files changed, 303 insertions, 122 deletions
@@ -1,3 +1,27 @@ +commit c9bcd8e68db61515080ff377c6a04fa807337258 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-06-17 16:36:13 +0200 + + Start with the generation of an input file + +commit e6f968cf97ed6ca9268e6098d86ba63ff2c6d2b0 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-05-24 16:07:35 +0200 + + Fix for the sawtooth function for repeated applications + + For n > 2, the second application was made at 2 * i instead of i. + +commit 4835e20d1d08203657ab616600286ad9dfd71344 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-05-24 15:46:44 +0200 + + Re-enable PELMO examples and tests + + - Add .gitattributes to make sure CRLF line endings are kept for PELMO + .psm files + - Update static docs + commit 539ea37b45ddc41b36dd199f06ffe5936ab13f21 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-05-17 12:23:38 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index fcefaa4..6173a49 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-3 -Date: 2017-05-24 -Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", +Date: 2017-06-19 +Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental concentrations (PECs) and for dealing with data from some FOCUS pesticide diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R index e6f2689..77839ab 100644 --- a/R/PEC_sw_focus.R +++ b/R/PEC_sw_focus.R @@ -1,10 +1,12 @@ -#' Calculate FOCUS Step 1 PEC surface water +#' Calculate PEC surface water at FOCUS Step 1 #' -#' 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 +#' This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, +#' authored by Michael Klein, in R. 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. +#' this implementation. Only Step 1 PECs are calculated. However, +#' input files are generated that are suitable as input also for Step 2 +#' to be used with the FOCUS calculator. #' #' @importFrom utils read.table #' @references FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). @@ -40,6 +42,12 @@ #' 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}} +#' @param region 'n' for Northern Europe or 's' for Southern Europe. If NA, only +#' Step 1 PECsw are calculated +#' @param season 'of' for October to February, 'mm' for March to May, and 'js' +#' for June to September. If NA, only step 1 PECsw are calculated +#' @param interception One of 'no interception' (default), 'minimal crop cover', +#' 'average crop cover' or 'full canopy' #' @param txt_file the name, and potentially the full path to the #' Steps.12 input text file to which the specification of the run(s) #' should be written @@ -48,11 +56,11 @@ #' @param append Should the input text file be appended? #' @examples #' # Parent only -#' dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8) +#' dummy_1 <- chent_focus_sw("Dummy 1", 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) +#' new_dummy <- chent_focus_sw("New Dummy", 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, @@ -60,6 +68,9 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, + region = c("n", "s"), + season = c(NA, "of", "mm", "js"), + interception = "no interception", txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE) { if (n > 1 & is.na(i)) stop("Please specify the interval i if n > 1") @@ -67,17 +78,17 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, if (is.na(f_drift)) { scenario = match.arg(scenario) f_drift = FOCUS_Step_12_scenarios$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 - # } + # For Step 2 we would select the reduced percentiles for multiple apps: + if (n <= 8) { + f_drift_2 = FOCUS_Step_12_scenarios$drift[scenario, as.character(n)] / 100 + } else { + f_drift_2 = FOCUS_Step_12_scenarios$drift[scenario, ">8"] / 100 + } } + interception = match.arg(interception) + # Write to txt file if requested - add_line <- function(x) cat(paste0(x, "\r\n"), file = txt, append = TRUE) - add <- function(x) cat(paste(x, "\t"), file = txt, append = TRUE) if (file.exists(txt_file)) { if (append) { txt <- file(txt_file, "a") @@ -89,52 +100,111 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, "appending or overwriting it") } } + } else { + txt <- file(txt_file, "w") } on.exit(close(txt)) + add_line <- function(x) cat(paste0(x, "\r\n"), file = txt, append = TRUE) # Write header to txt file - header <- c("Active Substance", "Compound", "Comment", "Mol mass a.i.", - "Mol mass met.", "Water solubility", "KOC assessed compound", - "KOC parent compound", "DT50", "Max. in Water", + header <- c("Active Substance", "Compound", "Comment", + "Mol mass a.i.", "Mol mass met.", + "Water solubility", + "KOC assessed compound", "KOC parent compound", + "DT50", + "Max. in Water", "Max. in Soil asessed compound", # we reproduce the typo... - "App. Rate", "Number of App.", "Time between app.", - "App. Type", "DT50 soil parent compound", "DT50 soil", - "DT50 water", "DT50 sediment", "Region / Season", + "App. Rate", "Number of App.", "Time between app.", "App. Type", + "DT50 soil parent compound", "DT50 soil", + "DT50 water", "DT50 sediment", + "Region / Season", "Interception class") add_line(paste(header, collapse = "\t")) - if (is.null(met)) { compound = parent$name cwsat = parent$cwsat mw_ratio = 1 max_soil = 1 max_ws = 1 - Koc = parent$Koc + Koc_assessed = parent$Koc DT50_ws = parent$DT50_ws + DT50_soil = parent$DT50_soil } else { compound = met$name cwsat = met$cwsat mw_ratio = met$mw / parent$mw max_soil = met$max_soil max_ws = met$max_ws - Koc = met$Koc + Koc_assessed = met$Koc DT50_ws = met$DT50_ws + DT50_soil = met$DT50_soil } - add(parent$name) - add(compound) - add(comment) - if (is.na(parent$mw)) add("-99.00") - else add(sprintf("%.2f", parent$mw)) - if (is.na(met$mw)) add("-99.00") - else add(sprintf("%.2f", met$mw)) - add(sprintf("%.2f", cwsat)) - add(sprintf("%.2f", Koc)) - if (is.null(met)) add("0.00E+00") - else add(sprintf("%.2f", parent$Koc)) - - # Rates for a single application + # In the Step 12 input file, the application type is the index of the drift + # scenarios, with numbering starting at 0 + app_type = which(scenario == rownames(FOCUS_Step_12_scenarios$drift)) - 1 + # The interception class is a number from 1.00 (no interception) to 4.00 (full canopy) + int_class = which(interception == colnames(FOCUS_Step_12_scenarios$interception)) + + # We calculate Step 2 if a season is specified + # Interception and region/season code + if (is.na(season[1])) { + f_int = 0 + reg_sea = 0 + } else { + f_int = FOCUS_Step_12_scenarios$interception[scenario, interception] + + # the code for region / season is the sum of the region code + reg_code = switch(region, + "n" = 0, + "s" = 3) + # and the season code + sea_code = switch(season, + "of" = 0, + "mm" = 1, + "js" = 2) + reg_sea = reg_code + sea_code + } + + run_txt <- c( + ai = parent$name, compound = compound, + comment = comment) + + run_numeric <- c( + mw_ai = NA, mw_met = NA, + cwsat = cwsat, Koc_assessed = Koc_assessed, Koc_parent = 0, + DT50_ws = DT50_ws, + max_ws = 0, max_soil = 0, + rate = rate, n = n, i = if(is.na(i)) 0 else i, + app_type = app_type, + DT50_soil_parent = 0, DT50_soil = 0, DT50_water = 0, DT50_sediment = 0, + reg_sea = reg_sea, int_class = int_class) + + if (is.null(met)) { + run_numeric["DT50_soil"] = parent$DT50_soil + run_numeric["DT50_water"] = parent$DT50_water + run_numeric["DT50_sediment"] = parent$DT50_sediment + } else { + run_numeric["mw_ai"] = parent$mw + run_numeric["mw_met"] = met$mw + run_numeric["Koc_parent"] = parent$Koc + run_numeric["DT50_soil"] = met$DT50_soil + run_numeric["DT50_soil_parent"] = parent$DT50_soil + run_numeric["DT50_water"] = met$DT50_water + run_numeric["DT50_sediment"] = met$DT50_sediment + } + + print_numeric <- function(x) { + ifelse(is.na(x), " -99.00", + ifelse(x < 0.01, + sprintf("%8.2E", x), + sprintf("%8.2f", x))) + } + run_line <- paste(c(run_txt, print_numeric(run_numeric)), collapse = "\t") + add_line(run_line) + + # Rates for a single application (suffix _s) 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 @@ -156,6 +226,7 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, input_rd_s = f_rd * eq_rate_rd_s_tot * ratio_field_wb / 10 input_rd = n * input_rd_s + # Step 1 accumulation in the aquatic system # No accumulation between multiple applications if 3 * DT50 < i if (n > 1 && (3 * DT50_ws < i)) { input_drift = input_drift_s @@ -165,13 +236,19 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, input_rd = n * input_rd_s } + # Step 2 accumulation in soil + # Use interception and degradation in soil for Step 2 + k_soil = log(2)/DT50_soil + f_deg_soil = exp(- 4 * k_soil) * # Four days of degradation + (1 - exp(-n * i * k_soil)) / (1 - exp(-i * k_soil)) # multiple applications + # Fraction of compound entering the water phase via runoff/drainage depth_sw = 0.3 # m depth_sed = 0.05 # m depth_sed_eff = 0.01 # m, only relevant for sorption rho_sed = 0.8 # kg/L f_OC = 0.05 # 5% organic carbon in sediment - f_rd_sw = depth_sw / (depth_sw + (depth_sed_eff * rho_sed * f_OC * Koc)) + f_rd_sw = depth_sw / (depth_sw + (depth_sed_eff * rho_sed * f_OC * Koc_assessed)) f_rd_sed = 1 - f_rd_sw # Initial PECs @@ -237,6 +314,9 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, #' @param name Length one character vector containing the name #' @param cwsat Water solubility in mg/L #' @param DT50_ws Half-life in water/sediment systems in days +#' @param DT50_soil Half-life in soil in days +#' @param DT50_water Half-life in water in days (Step 2) +#' @param DT50_sediment Half-life in sediment in days (Step 2) #' @param Koc Partition coefficient between organic carbon and water #' in L/kg. #' @param mw Molar weight in g/mol. @@ -244,8 +324,11 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA, #' @param max_ws Maximum observed fraction (dimensionless) in water/sediment #' systems #' @return A list with the substance specific properties -chent_focus_sw <- function(name, Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1) +chent_focus_sw <- function(name, Koc, DT50_ws = NA, DT50_soil = NA, + DT50_water = NA, DT50_sediment = NA, + cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1) { - list(Koc = Koc, DT50_ws = DT50_ws, cwsat = cwsat, + list(name = name, Koc = Koc, DT50_ws = DT50_ws, DT50_soil = DT50_soil, + DT50_water = DT50_water, DT50_sediment = DT50_sediment, cwsat = cwsat, mw = mw, max_soil = max_soil, max_ws = max_ws) } @@ -1,6 +1,9 @@ * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘pfm’: * checking DESCRIPTION meta-information ... OK +* excluding invalid files +Subdirectory 'R' contains invalid file names: + ‘pesticide.txt’ ‘xxx.txt’ * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added diff --git a/inst/testdata/Steps_12_pesticide.txt b/inst/testdata/Steps_12_pesticide.txt new file mode 100644 index 0000000..a2c3768 --- /dev/null +++ b/inst/testdata/Steps_12_pesticide.txt @@ -0,0 +1,12 @@ +Active Substance Compound Comment Mol mass a.i. Mol mass met. Water solubility KOC assessed compound KOC parent compound DT50 Max. in Water Max. in Soil asessed compound App. Rate Number of App. Time between app. App. Type DT50 soil parent compound DT50 soil DT50 water DT50 sediment Region / Season Interception class +Dummy 1 Dummy 1 Potatoes, Southern Europe, spring, 1 app/season, soil incorporation -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 100.00 100.00 3000.00 1.00 0.00E+00 28.00 1000.00 6.00 6.00 6.00 4.00 1.00 +Dummy 2 Dummy 2 Maize, Southern Europe, spring, 1 app/season 100.00 -99.00 30.00 110.00 0.00E+00 26.00 0.00E+00 0.00E+00 1000.00 1.00 0.00E+00 8.00 1000.00 56.00 26.00 26.00 4.00 1.00 +Dummy 3 Dummy 3 Winter wheat,, Northern Europe, spring, 1 app/season 0.00E+00 -99.00 620.00 1.00 0.00E+00 1.50 0.00E+00 0.00E+00 1000.00 1.00 0.00E+00 1.00 1000.00 4.00 1.50 1.50 1.00 1.00 +Dummy 4 Dummy 4 Apples, Southern Europe, spring, 3 app./season, 14 d int, orchards 0.00E+00 -99.00 2.00E-03 970.00 0.00E+00 4.00 0.00E+00 0.00E+00 7.50 3.00 14.00 12.00 1000.00 19.00 4.00 4.00 4.00 1.00 +Dummy 5 Dummy 5 Vines, Northern Europe, spring, 5 app/seaon 14 d int. 0.00E+00 -99.00 1.15 860.00 0.00E+00 118.00 0.00E+00 0.00E+00 75.00 5.00 14.00 23.00 1000.00 250.00 6.00 118.00 1.00 1.00 +Dummy 6 Dummy 6 Cereals, Northern Europe, spring, 1 app/season 0.00E+00 -99.00 6000.00 66.00 0.00E+00 24.00 0.00E+00 0.00E+00 400.00 1.00 0.00E+00 0.00E+00 1000.00 28.00 24.00 24.00 1.00 1.00 +Dummy 6 Dummy 6 Cereals, Southern Europe, spring, 1 app/seaon 0.00E+00 -99.00 200.00 66.00 0.00E+00 24.00 0.00E+00 0.00E+00 200.00 1.00 0.00E+00 0.00E+00 1000.00 28.00 24.00 24.00 4.00 1.00 +Dummy 7 Dummy 7 Vines, Southern Europe, spring, 4 app/seaon 14 d int. 0.00E+00 -99.00 2.60 500.00 0.00E+00 28.00 0.00E+00 0.00E+00 750.00 4.00 14.00 23.00 1000.00 50.00 2.50 28.00 4.00 1.00 +New Dummy Metabolite M1 Soil Metabolite 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 10.00 20.00 10.00 100.00 0.00E+00 1.00 +New Dummy Metabolite M2 Water Metabolite 250.00 100.00 100.00 50.00 100.00 100.00 50.00 0.00E+00 1000.00 1.00 0.00E+00 1.00 10.00 20.00 10.00 100.00 0.00E+00 1.00 +New Dummy Metabolite M3 Soil and Water Metabolite 250.00 100.00 100.00 50.00 100.00 100.00 50.00 50.00 1000.00 1.00 0.00E+00 1.00 10.00 20.00 10.00 100.00 0.00E+00 1.00 diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index a5628d7..e9f638d 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -2,11 +2,13 @@ % Please edit documentation in R/PEC_sw_focus.R \name{PEC_sw_focus} \alias{PEC_sw_focus} -\title{Calculate FOCUS Step 1 PEC surface water} +\title{Calculate PEC surface water at FOCUS Step 1} \usage{ -PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA, - f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, - txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE) +PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL, + f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, + region = c("n", "s"), season = c(NA, "of", "mm", "js"), + interception = "no interception", txt_file = "pesticide.txt", + overwrite = FALSE, append = TRUE) } \arguments{ \item{parent}{A list containing substance specific parameters, e.g. @@ -19,6 +21,8 @@ applications are given explicitly} \item{i}{The application interval} +\item{comment}{A comment for the input file} + \item{met}{A list containing metabolite specific parameters. e.g. conveniently generated by \code{\link{chent_focus_sw}}. If not NULL, the PEC is calculated for this compound, not the parent.} @@ -35,6 +39,15 @@ parent or a metabolite} \item{scenario}{The name of the scenario. Must be one of the scenario names given in \code{\link{FOCUS_Step_12_scenarios}}} +\item{region}{'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated} + +\item{season}{'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated} + +\item{interception}{One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'} + \item{txt_file}{the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) should be written} @@ -45,11 +58,13 @@ should be written} \item{append}{Should the input text file be appended?} } \description{ -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 +This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, +authored by Michael Klein, in R. 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. +this implementation. Only Step 1 PECs are calculated. However, +input files are generated that are suitable as input also for Step 2 +to be used with the FOCUS calculator. } \note{ The formulas for input to the waterbody via runoff/drainage of the @@ -63,11 +78,11 @@ Step 2 is not implemented. } \examples{ # Parent only -dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8) +dummy_1 <- chent_focus_sw("Dummy 1", 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) +new_dummy <- chent_focus_sw("New Dummy", 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) } diff --git a/man/chent_focus_sw.Rd b/man/chent_focus_sw.Rd index 945c343..8df01ab 100644 --- a/man/chent_focus_sw.Rd +++ b/man/chent_focus_sw.Rd @@ -4,18 +4,26 @@ \alias{chent_focus_sw} \title{Create a chemical compound object for FOCUS Step 1 calculations} \usage{ -chent_focus_sw(Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1, - max_ws = 1) +chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA, + DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1) } \arguments{ +\item{name}{Length one character vector containing the name} + \item{Koc}{Partition coefficient between organic carbon and water in L/kg.} \item{DT50_ws}{Half-life in water/sediment systems in days} +\item{DT50_soil}{Half-life in soil in days} + +\item{DT50_water}{Half-life in water in days (Step 2)} + +\item{DT50_sediment}{Half-life in sediment in days (Step 2)} + \item{cwsat}{Water solubility in mg/L} -\item{mw}{Molar weight in g/mol} +\item{mw}{Molar weight in g/mol.} \item{max_soil}{Maximum observed fraction (dimensionless) in soil} @@ -15,7 +15,7 @@ Simple PEC soil calculations: ........... Simple PEC surface water calculations with drift entry: .. Create PELMO runs from psm files and execute them: ........................................................................................................................................................................................................................... Actual and time weighted average concentrations for SFO kinetics: . -FOCUS Step 1 calculations: ......... +FOCUS Step 1 and 2 calculations: ........... Read and analyse TOXSWA cwa files: ....... UK drainage PEC calculations: ............ diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R index 0c8710b..2a65f36 100644 --- a/tests/testthat/test_step_1.R +++ b/tests/testthat/test_step_1.R @@ -1,125 +1,161 @@ -context("FOCUS Step 1 calculations") +context("FOCUS Step 1 and 2 calculations") -t_out <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1 test_txt <- readLines( system.file("testdata/Steps_12_pesticide.txt", package = "pfm") ) +# Define test compounds as in pesticide.txt +dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, DT50_soil = 6, Koc = 344.8, + DT50_water = 6, DT50_sediment = 6) +dummy_2 <- chent_focus_sw("Dummy 2", cwsat = 30, DT50_ws = 26, Koc = 110) +dummy_4 <- chent_focus_sw("Dummy 4", cwsat = 2e-3, DT50_ws = 4, Koc = 970) +dummy_5 <- chent_focus_sw("Dummy 5", cwsat = 1.15, DT50_ws = 118, Koc = 860) +dummy_7 <- chent_focus_sw("Dummy 7", cwsat = 2.60, DT50_ws = 28, Koc = 500) +new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) +M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, + Koc = 50, max_ws = 0, max_soil = 0.5) +M2 <- chent_focus_sw("M2", mw = 100, cwsat = 100, DT50_ws = 100, + Koc = 50, max_ws = 0.5, max_soil = 0) + +# When we compare the generated input file with the test file, +# we can ignore some fields +field_index <- c(ai = 1, compound = 2, comment = 3, + mw_ai = 4, mw_met = 5, + cwsat = 6, Koc_assessed = 7, + Koc_parent = 8, + DT50_ws = 9, + max_ws = 10, max_soil = 11, + rate = 12, n = 13, i = 14, app_type = 15, + DT50_soil_parent = 16, DT50_soil = 17, DT50_water = 18, DT50_sediment = 19, + reg_sea = 20, int_class = 21) +field_index_parent <- field_index[-c(4:5, 8, 10:11, 16)] + +t_out_1 <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1 +PEC_template_1 <- matrix(NA, nrow = length(t_out_1), ncol = 4, + dimnames = list(Time = t_out_1, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + +t_out_2 <- c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) # We read in text from rtf reports for Step 2 + test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", { - dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8) - res_dummy_1 <- PEC_sw_focus(dummy_1, 3000, + res_step_1_1 <- PEC_sw_focus(dummy_1, 3000, comment = "Potatoes, Southern Europe, spring, 1 app/season, soil incorporation", - f_drift = 0, + scenario = "no drift (incorp or seed trtmt)", + region = "s", season = "mm", append = FALSE, overwrite = TRUE) pest_txt <- readLines("pesticide.txt") - expect_equal(test_txt[1], pest_txt[1]) - strsplit(test_txt[2], "\t")[[1]] - - PEC_orig_1 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) - - PEC_orig_1[, "PECsw"] = c(685.06, 610.32, 543.73, 431.56) - PEC_orig_1[, "TWAECsw"] = c(NA, 647.69, 612.03, 548.76) - PEC_orig_1[, "PECsed"] = c(2.36, 2.1, 1.87, 1.49) * 1e3 - PEC_orig_1[, "TWAECsed"] = c(NA, 2.23e3, 2.11e3, 1.89e3) - - expect_equal(res_dummy_1$PEC[1:4, c(1, 2)], PEC_orig_1[, c(1, 2)], tolerance = 0.01, scale = 1) - expect_equal(res_dummy_1$PEC[1:4, c(3, 4)], PEC_orig_1[, c(3, 4)], tolerance = 10, scale = 1) + expect_equal(test_txt[1], pest_txt[1]) # Header + test_1 <- strsplit(test_txt[2], "\t")[[1]][field_index_parent] + pest_1 <- strsplit(pest_txt[2], "\t")[[1]][field_index_parent] + expect_equal(test_1, pest_1) # Parent fields + + PEC_step_1_1 <- PEC_template_1 + PEC_step_1_1[, "PECsw"] = c(685.06, 610.32, 543.73, 431.56) + PEC_step_1_1[, "TWAECsw"] = c(NA, 647.69, 612.03, 548.76) + PEC_step_1_1[, "PECsed"] = c(2.36, 2.1, 1.87, 1.49) * 1e3 + PEC_step_1_1[, "TWAECsed"] = c(NA, 2.23e3, 2.11e3, 1.89e3) + + expect_equal(res_step_1_1$PEC[1:4, c(1, 2)], PEC_step_1_1[, c(1, 2)], tolerance = 0.01, scale = 1) + expect_equal(res_step_1_1$PEC[1:4, c(3, 4)], PEC_step_1_1[, c(3, 4)], tolerance = 10, scale = 1) + + # This is pasted from the file "Dummy 1 step 2.rtf" generated with Steps12 version 3.2 from 15/05/2017 + PEC_step_2_1_raw <- read.table(text = "0 172.6235 NA 595.2057 NA +1 153.7900 163.2067 530.2680 562.7368 +2 137.0113 154.3037 472.4151 532.0392 +4 108.7460 138.3873 374.9561 477.1595 +7 76.8950 118.5090 265.1340 408.6191 +14 34.2528 85.6494 118.1038 295.3191 +21 15.2579 64.9380 52.6092 223.9062 +28 6.7966 51.3222 23.4348 176.9589 +42 1.3486 35.3389 4.6500 121.8484 +50 0.5352 29.8256 1.8454 102.8388 +100 0.0017 14.9591 0.0057 51.5788") + PEC_step_2_1 = PEC_step_2_1_raw[, 2:5] + dimnames(PEC_step_2_1) = list(Time = t_out_2, + type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")) + + # Step 2 is not implemented. }) test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", { - dummy_2 <- chent_focus_sw(cwsat = 30, DT50_ws = 26, Koc = 110) res_dummy_2 <- PEC_sw_focus(dummy_2, 1000) - PEC_orig_2 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_2 = PEC_template_1 - PEC_orig_2[, "PECsw"] = c(299.89, 290.86, 283.21, 268.50) - PEC_orig_2[, "TWAECsw"] = c(NA, 295.38, 291.20, 283.49) - PEC_orig_2[, "PECsed"] = c(319.77, 319.95, 311.53, 295.35) - PEC_orig_2[, "TWAECsed"] = c(NA, 319.86, 317.79, 310.58) + PEC_step_1_2[, "PECsw"] = c(299.89, 290.86, 283.21, 268.50) + PEC_step_1_2[, "TWAECsw"] = c(NA, 295.38, 291.20, 283.49) + PEC_step_1_2[, "PECsed"] = c(319.77, 319.95, 311.53, 295.35) + PEC_step_1_2[, "TWAECsed"] = c(NA, 319.86, 317.79, 310.58) - expect_equal(res_dummy_2$PEC[1:4, ], PEC_orig_2[, ], tolerance = 0.01, scale = 1) + expect_equal(res_dummy_2$PEC[1:4, ], PEC_step_1_2[, ], tolerance = 0.01, scale = 1) }) test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", { - dummy_4 <- chent_focus_sw(cwsat = 2e-3, DT50_ws = 4, Koc = 970) res_dummy_4 <- PEC_sw_focus(dummy_4, 7.5, n = 3, i = 14, scenario = "pome / stone fruit, early") - PEC_orig_4 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_4 = PEC_template_1 - PEC_orig_4[, "PECsw"] = c(1.82, 1.18, 1.00, 0.70) - PEC_orig_4[, "TWAECsw"] = c(NA, 1.50, 1.29, 1.07) - PEC_orig_4[, "PECsed"] = c(10.57, 11.49, 9.66, 6.83) - PEC_orig_4[, "TWAECsed"] = c(NA, 11.03, 10.79, 9.48) + PEC_step_1_4[, "PECsw"] = c(1.82, 1.18, 1.00, 0.70) + PEC_step_1_4[, "TWAECsw"] = c(NA, 1.50, 1.29, 1.07) + PEC_step_1_4[, "PECsed"] = c(10.57, 11.49, 9.66, 6.83) + PEC_step_1_4[, "TWAECsed"] = c(NA, 11.03, 10.79, 9.48) - expect_equal(res_dummy_4$PEC[1:4, ], PEC_orig_4[, ], tolerance = 0.01, scale = 1) + expect_equal(res_dummy_4$PEC[1:4, ], PEC_step_1_4[, ], tolerance = 0.01, scale = 1) }) test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", { - dummy_5 <- chent_focus_sw(cwsat = 1.15, DT50_ws = 118, Koc = 860) res_dummy_5 <- PEC_sw_focus(dummy_5, 75, n = 5, i = 14, scenario = "vines, early") - PEC_orig_5 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_5 = PEC_template_1 - PEC_orig_5[, "PECsw"] = c(61.60, 59.45, 59.10, 58.41) - PEC_orig_5[, "TWAECsw"] = c(NA, 60.53, 59.90, 59.33) - PEC_orig_5[, "PECsed"] = c(500.78, 511.28, 508.29, 502.35) - PEC_orig_5[, "TWAECsed"] = c(NA, 506.03, 507.90, 506.61) + PEC_step_1_5[, "PECsw"] = c(61.60, 59.45, 59.10, 58.41) + PEC_step_1_5[, "TWAECsw"] = c(NA, 60.53, 59.90, 59.33) + PEC_step_1_5[, "PECsed"] = c(500.78, 511.28, 508.29, 502.35) + PEC_step_1_5[, "TWAECsed"] = c(NA, 506.03, 507.90, 506.61) - expect_equal(res_dummy_5$PEC[1:4, ], PEC_orig_5[, ], tolerance = 0.01, scale = 1) + expect_equal(res_dummy_5$PEC[1:4, ], PEC_step_1_5[, ], tolerance = 0.01, scale = 1) }) test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", { - dummy_7 <- chent_focus_sw(cwsat = 2.60, DT50_ws = 28, Koc = 500) res_dummy_7 <- PEC_sw_focus(dummy_7, 750, n = 4, i = 14, scenario = "vines, early") - PEC_orig_7 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_7 = PEC_template_1 - PEC_orig_7[, "PECsw"] = c(626.99, 601.13, 586.43, 558.10) - PEC_orig_7[, "TWAECsw"] = c(NA, 614.06, 603.90, 588.03) - PEC_orig_7[, "PECsed"] = c(3.0, 3.01, 2.93, 2.79) * 1e3 - PEC_orig_7[, "TWAECsed"] = c(NA, 3.01e3, 2.99e3, 2.92e3) + PEC_step_1_7[, "PECsw"] = c(626.99, 601.13, 586.43, 558.10) + PEC_step_1_7[, "TWAECsw"] = c(NA, 614.06, 603.90, 588.03) + PEC_step_1_7[, "PECsed"] = c(3.0, 3.01, 2.93, 2.79) * 1e3 + PEC_step_1_7[, "TWAECsed"] = c(NA, 3.01e3, 2.99e3, 2.92e3) - expect_equal(res_dummy_7$PEC[1:4, c(1, 2)], PEC_orig_7[, c(1, 2)], tolerance = 0.01, scale = 1) - expect_equal(res_dummy_7$PEC[1:4, c(3, 4)], PEC_orig_7[, c(3, 4)], tolerance = 10, scale = 1) + expect_equal(res_dummy_7$PEC[1:4, c(1, 2)], PEC_step_1_7[, c(1, 2)], tolerance = 0.01, scale = 1) + expect_equal(res_dummy_7$PEC[1:4, c(3, 4)], PEC_step_1_7[, c(3, 4)], tolerance = 10, scale = 1) }) test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced", { - 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) res_M1 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1) - PEC_orig_M1 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_M1 = PEC_template_1 - PEC_orig_M1[, "PECsw"] = c(62.5, 62.07, 61.64, 60.79) - PEC_orig_M1[, "TWAECsw"] = c(NA, 62.28, 62.07, 61.64) - PEC_orig_M1[, "PECsed"] = c(31.25, 31.03, 30.82, 30.40) - PEC_orig_M1[, "TWAECsed"] = c(NA, 31.14, 31.03, 30.82) + PEC_step_1_M1[, "PECsw"] = c(62.5, 62.07, 61.64, 60.79) + PEC_step_1_M1[, "TWAECsw"] = c(NA, 62.28, 62.07, 61.64) + PEC_step_1_M1[, "PECsed"] = c(31.25, 31.03, 30.82, 30.40) + PEC_step_1_M1[, "TWAECsed"] = c(NA, 31.14, 31.03, 30.82) - expect_equal(res_M1$PEC[1:4, ], PEC_orig_M1[, ], tolerance = 0.01, scale = 1) + expect_equal(res_M1$PEC[1:4, ], PEC_step_1_M1[, ], tolerance = 0.01, scale = 1) - M2 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0.5, max_soil = 0) res_M2 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M2) - PEC_orig_M2 = matrix(NA, nrow = length(t_out), ncol = 4, - dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))) + PEC_step_1_M2 = PEC_template_1 - PEC_orig_M2[, "PECsw"] = c(64.34, 63.78, 63.34, 62.47) - PEC_orig_M2[, "TWAECsw"] = c(NA, 64.06, 63.81, 63.36) - PEC_orig_M2[, "PECsed"] = c(31.25, 31.89, 31.67, 31.23) - PEC_orig_M2[, "TWAECsed"] = c(NA, 31.57, 31.68, 31.56) + PEC_step_1_M2[, "PECsw"] = c(64.34, 63.78, 63.34, 62.47) + PEC_step_1_M2[, "TWAECsw"] = c(NA, 64.06, 63.81, 63.36) + PEC_step_1_M2[, "PECsed"] = c(31.25, 31.89, 31.67, 31.23) + PEC_step_1_M2[, "TWAECsed"] = c(NA, 31.57, 31.68, 31.56) - expect_equal(res_M2$PEC[1:4, ], PEC_orig_M2[, ], tolerance = 0.01, scale = 1) + expect_equal(res_M2$PEC[1:4, ], PEC_step_1_M2[, ], tolerance = 0.01, scale = 1) }) unlink("pesticide.txt") |