Add scenario, region and season to run name

5 files changed, 70 insertions, 25 deletions

diff --git a/ChangeLog b/ChangeLog
index 9f0c70c..428813b 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,36 @@
+commit 7df0f45b785841e9e490a945a9f6091a68e6333c
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-22 08:23:13 +0200
+
+    Add region and season to run name
+
+commit 0d60c88ba7e0693a832056ea3db5cc0eaf3b0819
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-20 14:16:14 +0200
+
+    Fix line endings and allow all interception classes
+
+commit dc1e49c8bb27cac81268719055bc4336843c0506
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-20 06:16:19 +0200
+
+    Keep dos format for pesticide.txt test data
+
+commit fd40f74907e89077bd81af5d779ae93e1434d8c6
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-20 06:11:12 +0200
+
+    Now the errors in PELMO output are gone - not reproducible
+
+commit 88044fd98c5b95d3f3f9bbef7416af66552189c1
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-20 06:04:14 +0200
+
+    Tests for Step 1 and 2 (input file only) pass, PELMO fails
+    
+    There are spurious errors in the output PELMO generates. Two examples
+    are in the test.log
+
 commit 34d4915297faf6236479f0e6474f8aa6b8d4b416
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-06-20 04:30:52 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index c456607..379f8a8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.4-3
-Date: 2017-06-20
+Date: 2017-06-22
 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/R/PEC_sw_focus.R b/R/PEC_sw_focus.R
index aed83a0..1dd5340 100644
--- a/R/PEC_sw_focus.R
+++ b/R/PEC_sw_focus.R
@@ -70,8 +70,8 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
   scenario = FOCUS_Step_12_scenarios$names,
   region = c("n", "s"),
   season = c(NA, "of", "mm", "js"),
-  interception = c("no interception", "minimal crop cover", 
-                   "average crop cover", "full canopy"), 
+  interception = c("no interception", "minimal crop cover",
+                   "average crop cover", "full canopy"),
   txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
 {
   if (n > 1 & is.na(i)) stop("Please specify the interval i if n > 1")
@@ -102,7 +102,7 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
               "DT50 water", "DT50 sediment",
               "Region / Season",
               "Interception class")
-  add_line <- function(x) cat(x, sep = "\r\n", 
+  add_line <- function(x) cat(x, sep = "\r\n",
                               file = txt, append = TRUE)
   if (file.exists(txt_file)) {
     if (append) {
@@ -169,8 +169,15 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
     reg_sea = reg_code + sea_code
   }
 
+  if (is.null(met)) {
+    name_input <- paste(parent$name, scenario, region, season)
+  } else {
+    name_input <- paste(met$name, scenario, region, season)
+  }
+  if (comment != "") name_input = paste(name_input, comment)
+
   run_txt <- c(
-    ai = parent$name, compound = compound,
+    ai = name_input, compound = name_input,
     comment = comment)
 
   run_numeric <- c(
diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index e9f638d..f55fccc 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -7,7 +7,8 @@
 PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL,
   f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
   region = c("n", "s"), season = c(NA, "of", "mm", "js"),
-  interception = "no interception", txt_file = "pesticide.txt",
+  interception = c("no interception", "minimal crop cover",
+  "average crop cover", "full canopy"), txt_file = "pesticide.txt",
   overwrite = FALSE, append = TRUE)
 }
 \arguments{
diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R
index 024a25a..23358dd 100644
--- a/tests/testthat/test_step_1.R
+++ b/tests/testthat/test_step_1.R
@@ -26,19 +26,6 @@ M2 <- chent_focus_sw("Metabolite M2",
                      Koc = 50, max_ws = 0.5, max_soil = 0,
                      DT50_soil = 20, DT50_water = 10, DT50_sediment = 100)
 
-# When we compare the generated input file with the test file,
-# we can ignore some fields if we are looking at the parent ai
-field_index <- c(ai = 1, compound = 2, comment = 3,
-  mw_ai = 4, mw_met = 5,
-  cwsat = 6, Koc_assessed = 7,
-  Koc_parent = 8,
-  DT50_ws = 9,
-  max_ws = 10, max_soil = 11,
-  rate = 12, n = 13, i = 14, app_type = 15,
-  DT50_soil_parent = 16, DT50_soil = 17, DT50_water = 18, DT50_sediment = 19,
-  reg_sea = 20, int_class = 21)
-field_index_parent <- field_index[-c(4:5, 8, 10:11, 16)]
-
 t_out_1 <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1
 PEC_template_1 <- matrix(NA, nrow = length(t_out_1), ncol = 4,
     dimnames = list(Time = t_out_1, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
@@ -176,6 +163,23 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M2) are reproduced"
 })
 
 context("FOCUS Steps 12 input files") # {{{1
+# When we compare the generated input file with the test file,
+# we can ignore some fields if we are looking at the parent ai
+# Also, the ai and compound names are not checked, as we append
+# scenario, region and season in order to get unique names
+# for Step 2 result files of the Step12 calculator
+field_index <- c(ai = 1, compound = 2, comment = 3,
+  mw_ai = 4, mw_met = 5,
+  cwsat = 6, Koc_assessed = 7,
+  Koc_parent = 8,
+  DT50_ws = 9,
+  max_ws = 10, max_soil = 11,
+  rate = 12, n = 13, i = 14, app_type = 15,
+  DT50_soil_parent = 16, DT50_soil = 17, DT50_water = 18, DT50_sediment = 19,
+  reg_sea = 20, int_class = 21)
+field_index_mets <- field_index[-c(1, 2)]
+field_index_parent <- field_index[-c(1:2, 4:5, 8, 10:11, 16)]
+
 test_that("Runs are correctly defined in the Steps 12 input file", { # {{{1
 
   pest_txt <- readLines("pesticide.txt")
@@ -207,14 +211,14 @@ test_that("Runs are correctly defined in the Steps 12 input file", { # {{{1
   expect_equal(test_7, pest_7) # Parent fields
 
   # New Dummy / M1
-  test_m1 <- strsplit(test_txt[10], "\t")[[1]]
-  pest_m1 <- strsplit(pest_txt[7], "\t")[[1]]
-  expect_equal(test_m1, pest_m1) # All fields
+  test_m1 <- strsplit(test_txt[10], "\t")[[1]][field_index_mets]
+  pest_m1 <- strsplit(pest_txt[7], "\t")[[1]][field_index_mets]
+  expect_equal(test_m1, pest_m1) # All fields except ai and met names
 
   # New Dummy / M2
-  test_m2 <- strsplit(test_txt[11], "\t")[[1]]
-  pest_m2 <- strsplit(pest_txt[8], "\t")[[1]]
-  expect_equal(test_m2, pest_m2) # All fields
+  test_m2 <- strsplit(test_txt[11], "\t")[[1]][field_index_mets]
+  pest_m2 <- strsplit(pest_txt[8], "\t")[[1]][field_index_mets]
+  expect_equal(test_m2, pest_m2) # All fields except ai and met names
 
 })
 unlink("pesticide.txt")