diff options
Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/print_sfo_saem_1.txt | 6 | ||||
| -rw-r--r-- | tests/testthat/summary_hfit_sfo_tc.txt | 2 | ||||
| -rw-r--r-- | tests/testthat/test_set_nd.R | 86 |
3 files changed, 90 insertions, 4 deletions
diff --git a/tests/testthat/print_sfo_saem_1.txt b/tests/testthat/print_sfo_saem_1.txt index a11e1e96..34eea058 100644 --- a/tests/testthat/print_sfo_saem_1.txt +++ b/tests/testthat/print_sfo_saem_1.txt @@ -7,13 +7,13 @@ Data: Likelihood computed by importance sampling AIC BIC logLik - 1311 1315 -649 + 1312 1316 -650 Fitted parameters: estimate lower upper -parent_0 1e+02 99.13 1e+02 +parent_0 1e+02 99.28 1e+02 k_parent 4e-02 0.03 4e-02 a.1 9e-01 0.75 1e+00 b.1 5e-02 0.04 5e-02 -SD.parent_0 7e-01 -1.09 3e+00 +SD.parent_0 2e-01 -6.33 7e+00 SD.k_parent 3e-01 0.20 4e-01 diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index ad701cee..e3e2f7e4 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -45,7 +45,7 @@ SD.log_k_parent 0.3 0.1 0.4 Variance model: est. lower upper -a.1 0.91 0.64 1.17 +a.1 0.90 0.64 1.17 b.1 0.05 0.04 0.06 Backtransformed parameters: 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) +}) |