Updates to pass checks and tests

9 files changed, 56 insertions, 14 deletions

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 5c3050c..f24b6bf 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -2,12 +2,14 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.2-3
-Date: 2015-07-02
+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: 'pfm' contains 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 0613a5c..cd2f08b 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -13,5 +13,6 @@ 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 7fd8ec1..9f729e5 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/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))