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-rw-r--r--ChangeLog28
-rw-r--r--DESCRIPTION2
-rw-r--r--test.log2
-rw-r--r--tests/testthat/test_step_1.R17
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)
})

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