Merge branch 'master' into pfm_chent

24 files changed, 81 insertions, 38 deletions

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 39b8c20..379cb3b 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -1,13 +1,15 @@
 Package: pfm
 Type: Package
-Title: Utilities for pesticide fate modelling
-Version: 0.2-1
-Date: 2015-06-12
+Title: Utilities for Pesticide Fate Modelling
+Version: 0.2-3
+Date: 2015-08-21
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", 
                   role = c("aut", "cre", "cph"))
-Description: Utilities for simple PEC calculations and for dealing with data
-  from some FOCUS pesticide fate modelling software.
+Description: Utilities for simple calculations of predicted environmental
+  concentrations (PECs) and for dealing with data from some FOCUS pesticide
+  fate modelling software packages.
 Depends: R6, mkin
+Imports: graphics
 Suggests: testthat
 License: GPL
 LazyLoad: yes
diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 4bc5fcf..1c879d1 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -1,6 +1,7 @@
-# Generated by roxygen2 (4.1.0.9001): do not edit by hand
+# Generated by roxygen2 (4.1.1): do not edit by hand
 
 S3method(plot,TOXSWA_cwa)
+export(PEC_pw)
 export(PEC_soil)
 export(PEC_soil_product)
 export(TOXSWA_cwa)
@@ -18,5 +19,6 @@ export(TOXSWA_cwa)
 export(geomean)
 export(pfm_degradation)
 export(read.TOXSWA_cwa)
+import(graphics)
 import(mkin)
 importFrom(R6,R6Class)
diff --git a/pkg/R/TOXSWA_cwa.R b/pkg/R/TOXSWA_cwa.R
index 55481b4..9e23284 100644
--- a/pkg/R/TOXSWA_cwa.R
+++ b/pkg/R/TOXSWA_cwa.R
@@ -58,6 +58,7 @@ read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL,
 #' Plot TOXSWA hourly concentrations of a chemical substance in a specific
 #' segment of a segment of a TOXSWA surface water body.
 #'
+#' @import graphics
 #' @param x The TOXSWA_cwa object to be plotted.
 #' @param xlab,ylab Labels for x and y axis.
 #' @param time_column What should be used for the time axis. If "t_firstjan" is chosen,
@@ -171,6 +172,7 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
       }
       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",
diff --git a/pkg/R/drift_data_JKI.R b/pkg/R/drift_data_JKI.R
index 44a959b..549798c 100644
--- a/pkg/R/drift_data_JKI.R
+++ b/pkg/R/drift_data_JKI.R
@@ -13,7 +13,7 @@
 #' @docType data
 #' @format A list currently containing matrices with spray drift percentage
 #' data for field crops (Ackerbau), and Pome/stone fruit, early and late
-#' (Obstbau früh, spät).
+#' (Obstbau frueh, spaet).
 #' @source JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved
 #' from
 #' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html
@@ -24,8 +24,8 @@
 #' \dontrun{
 #'   # This is the code that was used to extract the data
 #'   library(readxl)
-#'   abdrift_path <- "../inst/extdata/Tabelle der Abdrifteckwerte.xls"
-#'   JKI_crops <- c("Ackerbau", "Obstbau früh", "Obstbau spät")
+#'   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
+#'   JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
 #'   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
 #'   drift_data_JKI <- list()
 #' 
@@ -36,7 +36,7 @@
 #'                                             crop = JKI_crops)
 #'     drift_data_JKI[[n]] <- drift_data
 #'   }
-#'   save(drift_data_JKI, file = "../data/drift_data_JKI.RData")
+#'   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
 #' }
 #' 
 NULL
diff --git a/pkg/data/drift_data_JKI.RData b/pkg/data/drift_data_JKI.RData
index 061ca27..0a2f05e 100644
--- a/pkg/data/drift_data_JKI.RData
+++ b/pkg/data/drift_data_JKI.RData
diff --git a/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd
index 76ffd4b..1ced69a 100644
--- a/pkg/man/PEC_soil.Rd
+++ b/pkg/man/PEC_soil.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/PEC_soil.R
 \name{PEC_soil}
 \alias{PEC_soil}
diff --git a/pkg/man/PEC_sw_drainage_UK_ini.Rd b/pkg/man/PEC_sw_drainage_UK_ini.Rd
index 1b2009d..1715b39 100644
--- a/pkg/man/PEC_sw_drainage_UK_ini.Rd
+++ b/pkg/man/PEC_sw_drainage_UK_ini.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/PEC_sw_drainage_UK.R
 \name{PEC_sw_drainage_UK_ini}
 \alias{PEC_sw_drainage_UK_ini}
diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd
index 20299a5..99d3d65 100644
--- a/pkg/man/PEC_sw_drift.Rd
+++ b/pkg/man/PEC_sw_drift.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/PEC_sw_drift.R
 \name{PEC_sw_drift}
 \alias{PEC_sw_drift}
diff --git a/pkg/man/PEC_sw_drift_ini.Rd b/pkg/man/PEC_sw_drift_ini.Rd
index 0bcbf97..994a07e 100644
--- a/pkg/man/PEC_sw_drift_ini.Rd
+++ b/pkg/man/PEC_sw_drift_ini.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/PEC_sw_drift_ini.R
 \name{PEC_sw_drift_ini}
 \alias{PEC_sw_drift_ini}
diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd
index ee496d1..515562c 100644
--- a/pkg/man/PEC_sw_sed.Rd
+++ b/pkg/man/PEC_sw_sed.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/PEC_sw_sed.R
 \name{PEC_sw_sed}
 \alias{PEC_sw_sed}
diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd
index 967b60f..7a9c2f1 100644
--- a/pkg/man/SFO_actual_twa.Rd
+++ b/pkg/man/SFO_actual_twa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/SFO_actual_twa.R
 \name{SFO_actual_twa}
 \alias{SFO_actual_twa}
diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd
index 62a345b..0b441ae 100644
--- a/pkg/man/SSLRC_mobility_classification.Rd
+++ b/pkg/man/SSLRC_mobility_classification.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/SSLRC_mobility_classification.R
 \name{SSLRC_mobility_classification}
 \alias{SSLRC_mobility_classification}
diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd
index 5aa8bfc..b14f654 100644
--- a/pkg/man/TOXSWA_cwa.Rd
+++ b/pkg/man/TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \docType{class}
 \name{TOXSWA_cwa}
diff --git a/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd
index a2bbb77..d7e6d3b 100644
--- a/pkg/man/drift_data_JKI.Rd
+++ b/pkg/man/drift_data_JKI.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/drift_data_JKI.R
 \docType{data}
 \name{drift_data_JKI}
@@ -7,7 +7,7 @@
 published by the JKI}
 \format{A list currently containing matrices with spray drift percentage
 data for field crops (Ackerbau), and Pome/stone fruit, early and late
-(Obstbau früh, spät).}
+(Obstbau frueh, spaet).}
 \source{
 JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved
 from
@@ -27,8 +27,8 @@ as its licence is not clear.
 \dontrun{
   # This is the code that was used to extract the data
   library(readxl)
-  abdrift_path <- "../inst/extdata/Tabelle der Abdrifteckwerte.xls"
-  JKI_crops <- c("Ackerbau", "Obstbau früh", "Obstbau spät")
+  abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
+  JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
   drift_data_JKI <- list()
 
@@ -39,7 +39,7 @@ as its licence is not clear.
                                             crop = JKI_crops)
     drift_data_JKI[[n]] <- drift_data
   }
-  save(drift_data_JKI, file = "../data/drift_data_JKI.RData")
+  save(drift_data_JKI, file = "data/drift_data_JKI.RData")
 }
 }
 \keyword{datasets}
diff --git a/pkg/man/geomean.Rd b/pkg/man/geomean.Rd
index 42a30c4..be9f26a 100644
--- a/pkg/man/geomean.Rd
+++ b/pkg/man/geomean.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/geomean.R
 \name{geomean}
 \alias{geomean}
diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd
index b875434..04a692f 100644
--- a/pkg/man/pfm_degradation.Rd
+++ b/pkg/man/pfm_degradation.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/pfm_degradation.R
 \name{pfm_degradation}
 \alias{pfm_degradation}
diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd
index 1dddb78..8a5ada4 100644
--- a/pkg/man/plot.TOXSWA_cwa.Rd
+++ b/pkg/man/plot.TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \name{plot.TOXSWA_cwa}
 \alias{plot.TOXSWA_cwa}
diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd
index f67455f..684e107 100644
--- a/pkg/man/read.TOXSWA_cwa.Rd
+++ b/pkg/man/read.TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \name{read.TOXSWA_cwa}
 \alias{read.TOXSWA_cwa}
diff --git a/pkg/tests/testthat/H_sw_D4_pond.rds b/pkg/tests/testthat/H_sw_D4_pond.rds
deleted file mode 100644
index 62c54bc..0000000
--- a/pkg/tests/testthat/H_sw_D4_pond.rds
+++ /dev/null
diff --git a/pkg/tests/testthat/H_sw_D4_pond_printed.txt b/pkg/tests/testthat/H_sw_D4_pond_printed.txt
new file mode 100644
index 0000000..5730be6
--- /dev/null
+++ b/pkg/tests/testthat/H_sw_D4_pond_printed.txt
@@ -0,0 +1,10 @@
+<TOXSWA_cwa> data from file 00001p_pa.cwa segment 1 
+             datetime     t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L
+1 1985-01-01 00:00:00 0.000 0.00000000     -396.167    0.00000000        0.00000000
+2 1985-01-01 01:00:00 0.042 0.04166667     -396.125    0.08323064        0.08323716
+3 1985-01-01 02:00:00 0.083 0.08333333     -396.084    0.16626900        0.16628210
+4 1985-01-01 03:00:00 0.125 0.12500000     -396.042    0.24911240        0.24913190
+5 1985-01-01 04:00:00 0.167 0.16666667     -396.000    0.33172050        0.33174650
+6 1985-01-01 05:00:00 0.208 0.20833333     -395.959    0.41401430        0.41404670
+Moving window analysis
+NULL
diff --git a/pkg/tests/testthat/H_sw_R1_stream_events.rds b/pkg/tests/testthat/H_sw_R1_stream_events.rds
index 842c5de..ba6557b 100644
--- a/pkg/tests/testthat/H_sw_R1_stream_events.rds
+++ b/pkg/tests/testthat/H_sw_R1_stream_events.rds
diff --git a/pkg/tests/testthat/H_sw_R1_stream_printed.txt b/pkg/tests/testthat/H_sw_R1_stream_printed.txt
new file mode 100644
index 0000000..572ad6d
--- /dev/null
+++ b/pkg/tests/testthat/H_sw_R1_stream_printed.txt
@@ -0,0 +1,10 @@
+<TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
+               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L
+20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0                 0
+40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0                 0
+60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0                 0
+80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0                 0
+100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0                 0
+120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0                 0
+Moving window analysis
+NULL
diff --git a/pkg/tests/testthat/H_sw_R1_stream_windows.rds b/pkg/tests/testthat/H_sw_R1_stream_windows.rds
index 29e13f2..2531189 100644
--- a/pkg/tests/testthat/H_sw_R1_stream_windows.rds
+++ b/pkg/tests/testthat/H_sw_R1_stream_windows.rds
diff --git a/pkg/tests/testthat/test_TOXSWA_cwa.R b/pkg/tests/testthat/test_TOXSWA_cwa.R
index 582c51e..407a7a1 100644
--- a/pkg/tests/testthat/test_TOXSWA_cwa.R
+++ b/pkg/tests/testthat/test_TOXSWA_cwa.R
@@ -1,20 +1,37 @@
 library(pfm)
 context("Read and analyse TOXSWA cwa files")
 
-test_that("TOXSWA cwa file is correctly read", {
-  H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                   basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                   zipfile = system.file("testdata/SwashProjects.zip",
-                                               package = "pfm"))
-  H_sw_D4_pond$zipfile <- NULL # do not test the path
-  expect_equal_to_reference(H_sw_D4_pond, file = "H_sw_D4_pond.rds")
+zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm")
+basedir_test = "SwashProjects/project_H_sw/TOXSWA"
+
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = basedir_test,
+                                 zipfile = zipfile_test)
+
+H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                 basedir = basedir_test,
+                                 zipfile = zipfile_test)
+
+
+test_that("TOXSWA cwa file is correctly read and printed", {
+
+  # This was the setting when printing the output into text files
+  options(width = 100)
+
+  # Most content of the R6 object is at least partially printed
+
+  H_sw_D4_pond_printed <- capture.output(print(H_sw_D4_pond))
+
+  expect_equal(H_sw_D4_pond_printed, readLines("H_sw_D4_pond_printed.txt"))
+
+  H_sw_R1_stream_printed <- capture.output(print(H_sw_R1_stream))
+  expect_equal(H_sw_R1_stream_printed, readLines("H_sw_R1_stream_printed.txt"))
+
+  # The basedir is not printed, therefore tested separately
+  expect_equal(H_sw_D4_pond$basedir, basedir_test)
 })
 
 test_that("Getting events and moving window analysis works", {
-  H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
-                                   basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                   zipfile = system.file("testdata/SwashProjects.zip",
-                                               package = "pfm"))
 
   # Event analysis with two different thresholds
   H_sw_R1_stream$get_events(c(2, 10))