Start with the generation of an input file

3 files changed, 80 insertions, 6 deletions

diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R
index c098fb2..e6f2689 100644
--- a/R/PEC_sw_focus.R
+++ b/R/PEC_sw_focus.R
@@ -27,6 +27,7 @@
 #'   applications are given explicitly
 #' @param n The number of applications
 #' @param i The application interval
+#' @param comment A comment for the input file
 #' @param 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.
@@ -39,6 +40,12 @@
 #'   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 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
+#' @param overwrite Should an existing file a the location specified in
+#'   \code{txt_file} be overwritten?
+#' @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)
@@ -49,9 +56,11 @@
 #' 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,
+  comment = "",
   met = NULL,
   f_drift = NA, f_rd = 0.1,
-  scenario = FOCUS_Step_12_scenarios$names)
+  scenario = FOCUS_Step_12_scenarios$names,
+  txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
 {
   if (n > 1 & is.na(i)) stop("Please specify the interval i if n > 1")
 
@@ -66,7 +75,37 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
     # }
   }
 
+  # 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")
+    } else {
+      if (overwrite) {
+        txt <- file(txt_file, "w")
+      } else {
+        stop("The file", txt_file, "already exists, and you did not request",
+             "appending or overwriting it")
+      }
+    }
+  }
+  on.exit(close(txt))
+
+  # 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",
+              "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",
+              "Interception class")
+  add_line(paste(header, collapse = "\t"))
+
+
   if (is.null(met)) {
+    compound = parent$name
     cwsat = parent$cwsat
     mw_ratio = 1
     max_soil = 1
@@ -74,6 +113,7 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
     Koc = parent$Koc
     DT50_ws = parent$DT50_ws
   } else {
+    compound = met$name
     cwsat = met$cwsat
     mw_ratio = met$mw / parent$mw
     max_soil = met$max_soil
@@ -82,6 +122,18 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
     DT50_ws = met$DT50_ws
   }
 
+  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
   eq_rate_drift_s = mw_ratio * max_ws * rate
   # Parent only, or metabolite formed in soil:
@@ -182,16 +234,17 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
 #' Create a chemical compound object for FOCUS Step 1 calculations
 #'
 #' @export
+#' @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 Koc Partition coefficient between organic carbon and water
 #'   in L/kg.
-#' @param mw Molar weight in g/mol
+#' @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 = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)
+chent_focus_sw <- function(name, Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)
 {
   list(Koc = Koc, DT50_ws = DT50_ws, cwsat = cwsat,
        mw = mw, max_soil = max_soil, max_ws = max_ws)
diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index 7562b88..a5628d7 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -5,7 +5,8 @@
 \title{Calculate FOCUS Step 1 PEC surface water}
 \usage{
 PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA,
-  f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names)
+  f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
+  txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
 }
 \arguments{
 \item{parent}{A list containing substance specific parameters, e.g.
@@ -33,6 +34,15 @@ 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{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}
+
+\item{overwrite}{Should an existing file a the location specified in
+\code{txt_file} be overwritten?}
+
+\item{append}{Should the input text file be appended?}
 }
 \description{
 This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator
diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R
index 2be5df8..0c8710b 100644
--- a/tests/testthat/test_step_1.R
+++ b/tests/testthat/test_step_1.R
@@ -1,10 +1,20 @@
 context("FOCUS Step 1 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")
+)
 
 test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", {
-  dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8)
-  res_dummy_1 <- PEC_sw_focus(dummy_1, 3000, f_drift = 0)
+  dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8)
+  res_dummy_1 <- PEC_sw_focus(dummy_1, 3000,
+    comment = "Potatoes, Southern Europe, spring, 1 app/season, soil incorporation",
+    f_drift = 0,
+    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")))
@@ -112,3 +122,4 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced"
 
   expect_equal(res_M2$PEC[1:4, ], PEC_orig_M2[, ], tolerance = 0.01, scale = 1)
 })
+unlink("pesticide.txt")