From a0364c2561dda4c4b67e7e3b6830719b4ed60916 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 10 Nov 2022 12:17:34 +0100 Subject: 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. --- tests/testthat/test_set_nd.R | 86 -------------------------------------------- 1 file changed, 86 deletions(-) delete mode 100644 tests/testthat/test_set_nd.R (limited to 'tests') 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) -}) -- cgit v1.2.1