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authorJohannes Ranke <jranke@uni-bremen.de>2017-06-20 04:30:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2017-06-20 05:33:40 +0200
commit34d4915297faf6236479f0e6474f8aa6b8d4b416 (patch)
tree8a4b5f68ab95f9e18a2c1a4d4a51c6d38c79cd09 /R
parent7233eed00b799e08c31ae971f997b4b3c14eaea2 (diff)
Fix generation of input files
- Write header only if not appending - Write max_soil and max_ws for metabolites - Formatting
Diffstat (limited to 'R')
-rw-r--r--R/PEC_sw_focus.R39
1 files changed, 21 insertions, 18 deletions
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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