From 34d4915297faf6236479f0e6474f8aa6b8d4b416 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 20 Jun 2017 04:30:52 +0200
Subject: Fix generation of input files

- Write header only if not appending
- Write max_soil and max_ws for metabolites
- Formatting
---
 R/PEC_sw_focus.R | 39 +++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 18 deletions(-)

(limited to 'R/PEC_sw_focus.R')

diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R
index 77839ab..cbf182d 100644
--- a/R/PEC_sw_focus.R
+++ b/R/PEC_sw_focus.R
@@ -89,12 +89,26 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
   interception = match.arg(interception)
 
   # Write to txt file if requested
+  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 <- function(x) cat(paste0(x, "\r\n"), file = txt, append = TRUE)
   if (file.exists(txt_file)) {
     if (append) {
       txt <- file(txt_file, "a")
     } else {
       if (overwrite) {
         txt <- file(txt_file, "w")
+        add_line(paste(header, collapse = "\t"))
       } else {
         stop("The file", txt_file, "already exists, and you did not request",
              "appending or overwriting it")
@@ -102,24 +116,10 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
     }
   } else {
     txt <- file(txt_file, "w")
+    add_line(paste(header, collapse = "\t"))
   }
   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",
-              "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$name
@@ -188,6 +188,8 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
   } else {
     run_numeric["mw_ai"] = parent$mw
     run_numeric["mw_met"] = met$mw
+    run_numeric["max_soil"] = 100 * met$max_soil
+    run_numeric["max_ws"] = 100 * met$max_ws
     run_numeric["Koc_parent"] = parent$Koc
     run_numeric["DT50_soil"] = met$DT50_soil
     run_numeric["DT50_soil_parent"] = parent$DT50_soil
@@ -328,7 +330,8 @@ 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(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)
+  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)
 }
-- 
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