From d0a358a8f4fd03c95536409523e492eb15726f44 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 10:12:43 +0100 Subject: Review tests and examples based on winbuilder results Static documentation rebuilt by pkgdown --- tests/testthat/FOCUS_2006_D.csf | 2 +- tests/testthat/NAFTA_SOP_Appendix_B.txt | 26 +++++++++++++------------- tests/testthat/NAFTA_SOP_Appendix_D.txt | 30 +++++++++++++++--------------- tests/testthat/SFO_SFO_printed.txt | 1 - tests/testthat/test_mkinfit_errors.R | 1 + tests/testthat/test_mkinmod.R | 8 +++++--- tests/testthat/test_nafta.R | 7 ++++--- 7 files changed, 39 insertions(+), 36 deletions(-) (limited to 'tests') diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index ae524e01..c14aab4d 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2019-02-27 +Date: 2019-03-04 Optimiser: IRLS [Data] diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt index 3842db91..e5479b88 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_B.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt @@ -7,29 +7,29 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 51.2430312 1.178492e-10 45.4036817 57.0823806 -k_parent_sink 0.2531291 1.608492e-06 0.1935733 0.3310082 + Estimate Pr(>t) Lower Upper +parent_0 51.243 1.18e-10 45.404 57.082 +k_parent_sink 0.253 1.61e-06 0.194 0.331 $IORE - Estimate Pr(>t) Lower Upper -parent_0 51.710529483 8.522723e-15 4.951371e+01 53.907348241 -k__iore_parent_sink 0.001348359 6.841094e-02 3.421379e-04 0.005313859 -N_parent 2.661469429 3.975823e-08 2.191012e+00 3.131927092 + Estimate Pr(>t) Lower Upper +parent_0 51.71053 8.52e-15 4.95e+01 53.90735 +k__iore_parent_sink 0.00135 6.84e-02 3.42e-04 0.00531 +N_parent 2.66147 3.98e-08 2.19e+00 3.13193 $DFOP - Estimate Pr(>t) Lower Upper -parent_0 51.70546719 3.457982e-14 49.677926850 53.73300753 -k1 0.41569648 1.002119e-06 0.330769606 0.52242879 -k2 0.01273299 1.393989e-03 0.007230162 0.02242399 -g 0.83380396 5.718367e-12 0.771816175 0.88153694 + Estimate Pr(>t) Lower Upper +parent_0 51.7055 3.46e-14 49.67793 53.7330 +k1 0.4157 1.00e-06 0.33077 0.5224 +k2 0.0127 1.39e-03 0.00723 0.0224 +g 0.8338 5.72e-12 0.77182 0.8815 DTx values: DT50 DT90 DT50_rep SFO 2.74 9.1 2.74 IORE 1.37 28.5 8.57 -DFOP 2.17 39.9 54.40 +DFOP 2.17 39.9 54.44 Representative half-life: [1] 8.573302 diff --git a/tests/testthat/NAFTA_SOP_Appendix_D.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt index 8720a3b6..7ff2817c 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_D.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt @@ -7,29 +7,29 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 + Estimate Pr(>t) Lower Upper +parent_0 83.7558 8.08e-15 76.92822 90.58328 +k_parent_sink 0.0017 7.45e-05 0.00111 0.00262 $IORE - Estimate Pr(>t) Lower Upper -parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 -N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 + Estimate Pr(>t) Lower Upper +parent_0 9.69e+01 NA 8.75e+01 1.06e+02 +k__iore_parent_sink 8.40e-14 NA 1.09e-19 6.47e-08 +N_parent 6.68e+00 NA 3.54e+00 9.83e+00 $DFOP - Estimate Pr(>t) Lower Upper -parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 + Estimate Pr(>t) Lower Upper +parent_0 9.76e+01 4.44e-13 8.88e+01 1.06e+02 +k1 4.24e-02 3.55e-02 1.41e-02 1.27e-01 +k2 8.24e-04 2.06e-02 3.17e-04 2.14e-03 +g 2.88e-01 1.31e-04 1.78e-01 4.30e-01 DTx values: DT50 DT90 DT50_rep -SFO 407 1350 407 -IORE 541 5190000 1560000 -DFOP 429 2380 841 +SFO 407 1352 407 +IORE 541 5192060 1562966 +DFOP 429 2383 841 Representative half-life: [1] 841.4096 diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt index 8a188152..d0402fc0 100644 --- a/tests/testthat/SFO_SFO_printed.txt +++ b/tests/testthat/SFO_SFO_printed.txt @@ -6,7 +6,6 @@ $type: SFO; $to: m1; $sink: TRUE $m1 $type: SFO; $sink: TRUE Coefficient matrix $coefmat available -Compiled model $cf available Differential equations: d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R index 50d528e0..f1b4618c 100644 --- a/tests/testthat/test_mkinfit_errors.R +++ b/tests/testthat/test_mkinfit_errors.R @@ -81,6 +81,7 @@ test_that("We get reproducible output if quiet = FALSE", { }) test_that("We get warnings in case of overparameterisation", { + skip_on_cran() # On winbuilder the following fit does not give a warning expect_warning(f <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE), "not converge") s2 <- expect_warning(summary(mkinfit("DFOP", FOCUS_2006_A, quiet = TRUE)), "singular system") }) diff --git a/tests/testthat/test_mkinmod.R b/tests/testthat/test_mkinmod.R index 430fad61..1f8ec166 100644 --- a/tests/testthat/test_mkinmod.R +++ b/tests/testthat/test_mkinmod.R @@ -45,8 +45,10 @@ test_that("mkinmod stops to prevent and/or explain user errors", { }) test_that("Printing mkinmod models is reproducible", { - expect_known_output(print(mkinmod(parent = mkinsub("SFO", "m1"), - m1 = mkinsub("SFO"), - quiet = TRUE)), + m_test <- mkinmod(parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), + quiet = TRUE) + m_test$cf <- NULL # Remove to make test robust against missing gcc + expect_known_output(print(m_test), file = "SFO_SFO_printed.txt") }) diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index ad0f1d63..9528200d 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -19,10 +19,10 @@ context("Evaluations according to 2015 NAFTA guidance") test_that("Data for more than one compound are rejected", - expect_error(nafta(FOCUS_2006_D))) + expect_error(nafta(FOCUS_2006_D, cores = 1))) test_that("Test data from Appendix B are correctly evaluated", { - expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic")) + expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic", cores = 1)) # From Figure D.1 dtx_sop <- matrix(c(2.74, 1.37, 2.17, 9.1, 28.5, 39.9), nrow = 3, ncol = 2) @@ -43,7 +43,8 @@ test_that("Test data from Appendix B are correctly evaluated", { }) test_that("Test data from Appendix D are correctly evaluated", { - expect_message(res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555")) + expect_warning(res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555", + cores = 1, quiet = TRUE)) # From Figure D.1 dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2) -- cgit v1.2.1