Simplify tests where possible

4 files changed, 36 insertions, 13 deletions

diff --git a/ChangeLog b/ChangeLog
index 3297522..6f5775d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,31 @@
+commit d60bb9c0b52c8e0452bfbe507e60d5f651589cc8
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-16 18:57:16 +0200
+
+    Update static documentation
+
+commit 14fa47b1ea1651fc2cb7bbf0086741a8004d35ee
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-16 18:54:34 +0200
+
+    Remove external data also from git as their licence is unclear
+
+commit 608c4f89a2656f67ba915aab17633d41acc789a7
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-16 18:44:22 +0200
+
+    Add build and test logs to the git repo
+
+commit 3e26a8ab76a434c3465ea1db1b4a2a2ff3ea8ec8
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-16 18:40:25 +0200
+
+    Add TWA concentrations for days > 1, fix link
+    
+    Now we have seven test calculations for the Step 1 calculator, all
+    perfectly passing. This provides confidence that this is a
+    correct reimplementation of the Step 1 part of the Step 1/2 calculator.
+
 commit 36036b5901223591e7e21e8b73d8cd1fb034f4cb
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-05-16 15:43:50 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 8acf123..484970a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.4-3
-Date: 2017-05-16
+Date: 2017-05-17
 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/test.log b/test.log
index a880145..c94222b 100644
--- a/test.log
+++ b/test.log
@@ -15,7 +15,7 @@ Simple PEC soil calculations: ...........
 Simple PEC surface water calculations with drift entry: ..
 Create PELMO runs from psm files and execute them: SSSSS
 Actual and time weighted average concentrations for SFO kinetics: .
-FOCUS Step 1 calculations: ..............
+FOCUS Step 1 calculations: .........
 Read and analyse TOXSWA cwa files: .......
 UK drainage PEC calculations: ............
 
diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R
index 14045f5..2be5df8 100644
--- a/tests/testthat/test_step_1.R
+++ b/tests/testthat/test_step_1.R
@@ -1,6 +1,6 @@
 context("FOCUS Step 1 calculations")
 
-t_out <- c(0, 1, 2, 4) # Checking the first four days should be sufficient for Step 1
+t_out <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1
 
 test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", {
   dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8)
@@ -30,8 +30,7 @@ test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", {
   PEC_orig_2[, "PECsed"]  = c(319.77, 319.95, 311.53, 295.35)
   PEC_orig_2[, "TWAECsed"]  = c(NA, 319.86, 317.79, 310.58)
 
-  expect_equal(res_dummy_2$PEC[1:4, c(1, 2)], PEC_orig_2[, c(1, 2)], tolerance = 0.01, scale = 1)
-  expect_equal(res_dummy_2$PEC[1:4, c(3, 4)], PEC_orig_2[, c(3, 4)], tolerance = 0.01, scale = 1)
+  expect_equal(res_dummy_2$PEC[1:4, ], PEC_orig_2[, ], tolerance = 0.01, scale = 1)
 })
 
 test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", {
@@ -47,8 +46,7 @@ test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", {
   PEC_orig_4[, "PECsed"]  = c(10.57, 11.49, 9.66, 6.83)
   PEC_orig_4[, "TWAECsed"]  = c(NA, 11.03, 10.79, 9.48)
 
-  expect_equal(res_dummy_4$PEC[1:4, c(1, 2)], PEC_orig_4[, c(1, 2)], tolerance = 0.01, scale = 1)
-  expect_equal(res_dummy_4$PEC[1:4, c(3, 4)], PEC_orig_4[, c(3, 4)], tolerance = 0.01, scale = 1)
+  expect_equal(res_dummy_4$PEC[1:4, ], PEC_orig_4[, ], tolerance = 0.01, scale = 1)
 })
 
 test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", {
@@ -64,8 +62,7 @@ test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", {
   PEC_orig_5[, "PECsed"]  = c(500.78, 511.28, 508.29, 502.35)
   PEC_orig_5[, "TWAECsed"]  = c(NA, 506.03, 507.90, 506.61)
 
-  expect_equal(res_dummy_5$PEC[1:4, c(1, 2)], PEC_orig_5[, c(1, 2)], tolerance = 0.01, scale = 1)
-  expect_equal(res_dummy_5$PEC[1:4, c(3, 4)], PEC_orig_5[, c(3, 4)], tolerance = 0.01, scale = 1)
+  expect_equal(res_dummy_5$PEC[1:4, ], PEC_orig_5[, ], tolerance = 0.01, scale = 1)
 })
 
 test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", {
@@ -99,8 +96,7 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced"
   PEC_orig_M1[, "PECsed"]  = c(31.25, 31.03, 30.82, 30.40)
   PEC_orig_M1[, "TWAECsed"]  = c(NA, 31.14, 31.03, 30.82)
 
-  expect_equal(res_M1$PEC[1:4, c(1, 2)], PEC_orig_M1[, c(1, 2)], tolerance = 0.01, scale = 1)
-  expect_equal(res_M1$PEC[1:4, c(3, 4)], PEC_orig_M1[, c(3, 4)], tolerance = 0.01, scale = 1)
+  expect_equal(res_M1$PEC[1:4, ], PEC_orig_M1[, ], tolerance = 0.01, scale = 1)
 
   M2 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0.5, max_soil = 0)
   res_M2 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter",
@@ -114,6 +110,5 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced"
   PEC_orig_M2[, "PECsed"]  = c(31.25, 31.89, 31.67, 31.23)
   PEC_orig_M2[, "TWAECsed"]  = c(NA, 31.57, 31.68, 31.56)
 
-  expect_equal(res_M2$PEC[1:4, c(1, 2)], PEC_orig_M2[, c(1, 2)], tolerance = 0.01, scale = 1)
-  expect_equal(res_M2$PEC[1:4, c(3, 4)], PEC_orig_M2[, c(3, 4)], tolerance = 0.01, scale = 1)
+  expect_equal(res_M2$PEC[1:4, ], PEC_orig_M2[, ], tolerance = 0.01, scale = 1)
 })