From c9bcd8e68db61515080ff377c6a04fa807337258 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 17 Jun 2017 16:36:13 +0200
Subject: Start with the generation of an input file

---
 R/PEC_sw_focus.R | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 56 insertions(+), 3 deletions(-)

(limited to 'R/PEC_sw_focus.R')

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)
-- 
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