Adapt to TOXSWA 5.5.3

4 files changed, 25 insertions, 8 deletions

diff --git a/ChangeLog b/ChangeLog
index 7ea31a7..926bcd6 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+commit bd15236d5dedb4067bd29e58e655c5352aca1db4
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2018-06-08 16:20:40 +0200
+
+    Enable PEC porewater for the default scenario
+    
+    The default scenario uses soil parameters from the REACH guidance R.16,
+    Table R.16-9.
+
 commit ec2052d68950745380c2724757b3ba8b116605fc
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2018-06-08 14:54:40 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 96aea24..0851224 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
-Version: 0.4-5
-Date: 2018-06-08
+Version: 0.4-6
+Date: 2018-06-11
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R
index 4caafb6..576c7d3 100644
--- a/R/TOXSWA_cwa.R
+++ b/R/TOXSWA_cwa.R
@@ -259,17 +259,25 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
           stop("Could not read ", filename)
         }
       } else {
-        # out file from FOCUS TOXSWA 4 (TOXSWA 4.4.2 or similar)
+        # out file from FOCUS TOXSWA 4 or higher
         outfile <- try(readLines(file_connection))
 
+        focus_toxswa_version <- gsub(".*: ", "", outfile[4])
+
+        if (substr(focus_toxswa_version, 1, 1) == "3") {
+          cwastring = "ConLiqWatLayCur"
+        } else {
+          cwastring = "ConLiqWatLay"
+        }
+
         close(file_connection) # only needed for files
 
         if (inherits(outfile, "try-error")) {
           stop("Could not read ", filename)
         } else {
           # Get the substance name(s)
-          sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE)
-          substances <- gsub(".*ConLiqWatLayCur_(.*?) +[0-9].*", "\\1", sub_lines)
+          sub_lines <- grep(paste0(".*0.000.*", cwastring, "_"), outfile[1:50], value = TRUE)
+          substances <- gsub(paste0(".*", cwastring, "_(.*?) +[0-9].*"), "\\1", sub_lines)
           if (!substance %in% c("parent", substances)) {
             stop("No data for substance ", substance, " present in the .out file.")
           }
@@ -277,9 +285,9 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
           # Generate field name for the concentrations at end of hour for the
           # substance of interest
           if (substance == "parent") {
-            cwa_string = paste0("ConLiqWatLayCur_", substances[1])
+            cwa_string = paste0(cwastring, "_", substances[1])
           } else {
-            cwa_string = paste0("ConLiqWatLayCur_", substance)
+            cwa_string = paste0(cwastring, "_", substance)
           }
 
           cwa_lines <- grep(cwa_string, outfile, value = TRUE)
diff --git a/build.log b/build.log
index 95a265b..ea12067 100644
--- a/build.log
+++ b/build.log
@@ -4,5 +4,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 * looking to see if a ‘data/datalist’ file should be added
-* building ‘pfm_0.4-5.tar.gz’
+* building ‘pfm_0.4-6.tar.gz’