Improve reading spead for new TOXSWA format

7 files changed, 28 insertions, 16 deletions

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 1cc6817..ab3e92a 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -13,7 +13,8 @@ Depends:
     mkin
 Imports:
     graphics,
-    chents
+    chents,
+    readr
 Suggests:
     testthat
 License: GPL
diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 0632e51..c59559b 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -24,3 +24,5 @@ import(chents)
 import(graphics)
 import(mkin)
 importFrom(R6,R6Class)
+importFrom(readr,fwf_empty)
+importFrom(readr,read_fwf)
diff --git a/pkg/R/TOXSWA_cwa.R b/pkg/R/TOXSWA_cwa.R
index 46b1995..a693dc1 100644
--- a/pkg/R/TOXSWA_cwa.R
+++ b/pkg/R/TOXSWA_cwa.R
@@ -34,6 +34,7 @@
 #'   maximum time weighted average concentrations and areas under the curve.
 #' @param thresholds Numeric vector of threshold concentrations in µg/L for
 #'   generating event statistics.  
+#' @importFrom readr read_fwf fwf_empty
 #' @return An instance of an R6 object of class
 #' \code{\link{TOXSWA_cwa}}.
 #' @export
@@ -174,17 +175,18 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
       } else {
         try(file_connection <- file(file.path(basedir, filename), "rt"))
       }
+      
 
       if (grepl(".cwa$", filename)) {
         # cwa file from FOCUS TOXSWA 3 (TOXSWA 2.x.y)
-        cwa_all_segments <- try(read.table(file_connection,
-                                           sep = "", skip = 40, 
-                                           encoding = "UTF-8",
-                                           colClasses = c("character", "numeric",
-                                                          "integer", rep("numeric", 5)),
-                                           col.names = c("datetime", "t", "segment",
-                                                         "xcd", "cwa_tot", "cwa",
-                                                         "Xss", "Xmp")))
+        cwa_all_segments <- try(
+          read.table(file_connection,
+          sep = "", skip = 40,
+          encoding = "UTF-8",
+          colClasses = c("character", "numeric",
+                         "integer", rep("numeric", 5)),
+          col.names = c("datetime", "t", "segment",
+                        "xcd", "cwa_tot", "cwa", "Xss", "Xmp")))
         if (is.null(zipfile)) close(file_connection) # only needed for files
 
         if (!inherits(cwa_all_segments, "try-error")) {
@@ -225,15 +227,17 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
           stop("Could not read ", filename)
         } else {
           cwa_lines <- outfile[grep("ConLiqWatLay_", outfile)] # hourly concentrations
-          cwa_all_segments <- read.table(text = cwa_lines) 
+
+          cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), 
+                                       fwf_empty(paste(tail(cwa_lines), collapse = "\n")))
 
           available_segments = 1:(ncol(cwa_all_segments) - 3)
           if (segment == "last") segment = max(available_segments)
           if (!segment %in% available_segments) stop("Invalid segment specified")
           self$segment <- segment
           cwa <- data.frame(
-            datetime = as.character(cwa_all_segments$V2),
-            t = cwa_all_segments$V1,
+            datetime = as.character(cwa_all_segments$X2),
+            t = cwa_all_segments$X1,
             cwa = cwa_all_segments[[3 + segment]]
           )
           if (total) {
diff --git a/pkg/inst/testdata/SwashProjects.zip b/pkg/inst/testdata/SwashProjects.zip
index 49507c9..5b9ff49 100644
--- a/pkg/inst/testdata/SwashProjects.zip
+++ b/pkg/inst/testdata/SwashProjects.zip
diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd
index c486831..6a1b935 100644
--- a/pkg/man/PEC_sw_drift.Rd
+++ b/pkg/man/PEC_sw_drift.Rd
@@ -6,7 +6,7 @@
 \usage{
 PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_data = "JKI",
   crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha",
-  PEC_units = "µg/L")
+  PEC_units = "<U+00B5>g/L")
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd
index 3140eb0..d0e2ec6 100644
--- a/pkg/man/PEC_sw_sed.Rd
+++ b/pkg/man/PEC_sw_sed.Rd
@@ -7,7 +7,7 @@ water concentrations}
 \usage{
 PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
   sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
-  PEC_sed_units = c("µg/kg", "mg/kg"))
+  PEC_sed_units = c("<U+00B5>g/kg", "mg/kg"))
 }
 \arguments{
 \item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for
diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd
index acc384c..44a7542 100644
--- a/pkg/man/read.TOXSWA_cwa.Rd
+++ b/pkg/man/read.TOXSWA_cwa.Rd
@@ -5,10 +5,11 @@
 \title{Read TOXSWA surface water concentrations}
 \usage{
 read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
-  windows = NULL, thresholds = NULL)
+  total = FALSE, windows = NULL, thresholds = NULL)
 }
 \arguments{
-\item{filename}{The filename of the cwa file.}
+\item{filename}{The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
+out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).}
 
 \item{basedir}{The path to the directory where the cwa file resides.}
 
@@ -17,6 +18,10 @@ read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
 \item{segment}{The segment for which the data should be read. Either "last", or 
 the segment number.}
 
+\item{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.}
+
 \item{windows}{Numeric vector of width of moving windows in days, for calculating
 maximum time weighted average concentrations and areas under the curve.}