Add set_nd_nq previously in pfm

pfm depends on mkin anyways, so reexporting set_nd_nq and
set_nd_nq_focus in pfm should provide reasonable continuity.

1 files changed, 86 insertions, 0 deletions

diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R
new file mode 100644
index 00000000..232e7c62
--- /dev/null
+++ b/tests/testthat/test_set_nd.R
@@ -0,0 +1,86 @@
+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)
+})