set_nd_nq is now in mkin, fix Steps12 bug

If a scenario with a slash "/" was selected in PEC_sw_focus(),
the Step 2 file generated giving an error (path not found) in the
Steps12 calculator, because the scenario name is part of the "compound"
name in this implementation, in order to show it in the list that the
calculator presents.

1 files changed, 0 insertions, 86 deletions

diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R
deleted file mode 100644
index 232e7c6..0000000
--- a/tests/testthat/test_set_nd.R
+++ /dev/null
@@ -1,86 +0,0 @@
-context("Processing of residue series")
-
-# FOCUS (2014) page 76 (parent) and page 132 (metabolite)
-
-parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-
-test_that("Simple residue series are processed as intended", {
-
-  expect_equal(set_nd_nq(parent_1, 0.02),
-    c(.12, .09, .05, .03, .01, rep(NA, 5)))
-
-  expect_equal(set_nd_nq(parent_2, 0.02, loq = 0.05),
-    c(.12, .09, .05, .03, .01, .01, .03, .01, NA, NA))
-
-  expect_equal(set_nd_nq(metabolite, 0.02, loq = 0.05),
-    c(NA, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
-
-  expect_equal(set_nd_nq(c("nd", 1, 0.2, "nd"), 0.1),
-    c(NA, 1, 0.2, 0.05))
-
-})
-
-test_that("Simple residue series are processed as in the FOCUS guidance", {
-
-  # Parent 1
-  expect_error(set_nd_nq_focus(parent_1, 0.02),
-    "You need to specify an LOQ")
-  expect_equal(set_nd_nq_focus(parent_1, 0.02, 0.05),
-    c(.12, .09, .05, .03, .01, rep(NA, 5)))
-
-  # Parent 2
-  expect_equal(set_nd_nq_focus(parent_2, 0.02, loq = 0.05),
-    c(.12, .09, .05, .03, .01, rep(NA, 5)))
-
-  # Parent 3
-  expect_equal(set_nd_nq_focus(parent_3, 0.02, loq = 0.05),
-    c(.12, .09, .05, .03, .01, .01, .06, .01, NA, NA))
-
-  # Metabolite
-  expect_equal(set_nd_nq_focus(metabolite, 0.02, loq = 0.05),
-    c(0, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
-
-})
-
-test_that("Examples Boesten et al. (2015, p. 57/58) are correctly processed", {
-  table_8 <- matrix(
-    c(10, 10, rep("nd", 4),
-      10, 10, rep("nq", 2), rep("nd", 2),
-      10, 10, 10, "nq", "nd", "nd",
-      "nq", 10, "nq", rep("nd", 3),
-      "nd", "nq", "nq", rep("nd", 3),
-      rep("nd", 6), rep("nd", 6)),
-    ncol = 6, byrow = TRUE)
-  table_8_processed <- set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
-  table_9 <- matrix(
-    c(10, 10, 0.25, 0.25, NA, NA,
-      10, 10, 1, 1, 0.25, NA,
-      10, 10, 10, 1, 0.25, NA,
-      1, 10, 1, 0.25, NA, NA,
-      0.25, 1, 1, 0.25, NA, NA,
-      NA, 0.25, 0.25, NA, NA, NA,
-      rep(NA, 6)),
-    ncol = 6, byrow = TRUE)
-  expect_equal(table_8_processed, table_9)
-
-  table_10 <- matrix(
-    c(10, 10, rep("nd", 4),
-      10, 10, rep("nd", 4),
-      10, 10, 10, rep("nd", 3),
-      "nd", 10, rep("nd", 4),
-      rep("nd", 18)),
-    ncol = 6, byrow = TRUE)
-  table_10_processed <- set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
-  table_11 <- matrix(
-    c(10, 10, 0.25, rep(NA, 3),
-      10, 10, 0.25, rep(NA, 3),
-      10, 10, 10, 0.25, NA, NA,
-      0.25, 10, 0.25, rep(NA, 3),
-      NA, 0.25, rep(NA, 4),
-      rep(NA, 12)),
-    ncol = 6, byrow = TRUE)
-  expect_equal(table_10_processed, table_11)
-})