diff options
Diffstat (limited to 'tests/testthat/test_set_nd.R')
| -rw-r--r-- | tests/testthat/test_set_nd.R | 64 |
1 files changed, 53 insertions, 11 deletions
diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R index 6b73e2d..232e7c6 100644 --- a/tests/testthat/test_set_nd.R +++ b/tests/testthat/test_set_nd.R @@ -1,4 +1,5 @@ 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") @@ -6,39 +7,80 @@ 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 processed as intended", { +test_that("Simple residue series are processed as intended", { - expect_equal(set_nd(parent_1, 0.02), + expect_equal(set_nd_nq(parent_1, 0.02), c(.12, .09, .05, .03, .01, rep(NA, 5))) - expect_equal(set_nd(parent_2, 0.02, loq = 0.05), + 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(metabolite, 0.02, loq = 0.05), + 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(c("nd", 1, 0.2, "nd"), 0.1), c(NA, 1, 0.2, 0.05)) + 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_focus(parent_1, 0.02), - "You need to specify an loq") - expect_equal(set_nd_focus(parent_1, 0.02, 0.05), + 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_focus(parent_2, 0.02, loq = 0.05), + 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_focus(parent_3, 0.02, loq = 0.05), + 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_focus(metabolite, 0.02, loq = 0.05), + 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) +}) |