diff options
| -rw-r--r-- | pkg/DESCRIPTION | 4 | ||||
| -rw-r--r-- | pkg/R/TOXSWA_cwa.R | 32 |
2 files changed, 29 insertions, 7 deletions
diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION index e24d04f..e3f29cc 100644 --- a/pkg/DESCRIPTION +++ b/pkg/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.3-6 -Date: 2016-07-15 +Version: 0.3-7 +Date: 2016-07-30 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental diff --git a/pkg/R/TOXSWA_cwa.R b/pkg/R/TOXSWA_cwa.R index fd056b2..c5ddce9 100644 --- a/pkg/R/TOXSWA_cwa.R +++ b/pkg/R/TOXSWA_cwa.R @@ -19,7 +19,7 @@ #' #' Read TOXSWA hourly concentrations of a chemical substance in a specific #' segment of a TOXSWA surface water body. Per default, the data for the last -#' segment are imported. As TOXSWA reports the values at the end of the hour +#' segment are imported. As TOXSWA 4 reports the values at the end of the hour #' (ConLiqWatLayCur) in its summary file, we use this value as well instead #' of the hourly averages (ConLiqWatLay). #' @@ -32,6 +32,9 @@ #' @param total Set this to TRUE in order to read total concentrations as well. This is #' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa #' files. For .cwa files, the total concentration is always read as well. +#' @param substance For TOXSWA 4 .out files, the default value "parent" leads +#' to reading concentrations of the parent compound. Alternatively, the substance +#' of interested can be selected by its code name. #' @param windows Numeric vector of width of moving windows in days, for calculating #' maximum time weighted average concentrations and areas under the curve. #' @param thresholds Numeric vector of threshold concentrations in µg/L for @@ -47,11 +50,13 @@ #' zipfile = system.file("testdata/SwashProjects.zip", #' package = "pfm")) read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL, - segment = "last", total = FALSE, + segment = "last", substance = "parent", + total = FALSE, windows = NULL, thresholds = NULL) { if (!missing(filename)) { - cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, total = total) + cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, + substance = substance, total = total) if (!is.null(windows[1])) cwa$moving_windows(windows) if (!is.null(thresholds[1])) cwa$get_events(thresholds) invisible(cwa) @@ -165,10 +170,12 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", basedir = NULL, zipfile = NULL, segment = NULL, + substance = NULL, cwas = NULL, windows = NULL, events = list(), - initialize = function(filename, basedir, zipfile = NULL, segment = "last", total = FALSE) { + initialize = function(filename, basedir, zipfile = NULL, + segment = "last", substance = "parent", total = FALSE) { self$filename <- filename self$basedir <- basedir self$zipfile <- zipfile @@ -227,7 +234,22 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", if (inherits(outfile, "try-error")) { stop("Could not read ", filename) } else { - cwa_lines <- outfile[grep("ConLiqWatLayCur_", outfile)] # concentrations at end of hour + # Get the substance name(s) + sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE) + substances <- gsub(".*ConLiqWatLayCur_(.*?) *[0-9].*", "\\1", sub_lines) + if (!substance %in% c("parent", substances)) { + stop("No data for substance ", substance, " present in the .out file.") + } + + # Generate field name for the concentrations at end of hour for the + # substance of interest + if (substance == "parent") { + cwa_string = paste0("ConLiqWatLayCur_", substances[1]) + } else { + cwa_string = paste0("ConLiqWatLayCur_", substance) + } + + cwa_lines <- grep(cwa_string, outfile, value = TRUE) cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), fwf_empty(paste(tail(cwa_lines), collapse = "\n"))) |