diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/setup_script.R | 16 | ||||
| -rw-r--r-- | tests/testthat/test_FOCUS_D_UBA_expertise.R | 10 | ||||
| -rw-r--r-- | tests/testthat/test_SFORB.R | 5 | ||||
| -rw-r--r-- | tests/testthat/test_analytical.R | 5 | ||||
| -rw-r--r-- | tests/testthat/test_error_models.R | 17 | ||||
| -rw-r--r-- | tests/testthat/test_nafta.R | 5 | ||||
| -rw-r--r-- | tests/testthat/test_synthetic_data_for_UBA_2014.R | 23 |
8 files changed, 51 insertions, 32 deletions
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index f845cc1d..7c8340cd 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: 2020-05-28 +Date: 2020-05-29 Optimiser: IRLS [Data] diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index def52697..8d8ba3e9 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -57,18 +57,26 @@ DFOP_SFO <- mkinmod(parent = mkinsub("DFOP", to = "m1"), # Avoid warning when fitting a dataset where zero value is removed FOCUS_D <- subset(FOCUS_2006_D, value != 0) +# We do not want warnings about non-normality of residuals here +suppressWarnings( f_sfo_sfo_desolve <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) +) +suppressWarnings( f_sfo_sfo_eigen <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "eigen", quiet = TRUE) - +) +suppressWarnings( f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) +) SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data -f_2_mkin <- mkinfit("DFOP", DFOP_par_c, quiet = TRUE) +# We also suppress the warning about non-normality of residuals here, the data +# were generated with a different error model, so no wonder! +f_2_mkin <- suppressWarnings(mkinfit("DFOP", DFOP_par_c, quiet = TRUE)) f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = subset(DFOP_par_c, name == "parent")) f_2_anova <- lm(value ~ as.factor(time), data = subset(DFOP_par_c, name == "parent")) @@ -86,9 +94,9 @@ m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), fit_nw_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE) -# We know direct optimization is OK and direct needs 4 sec versus 5.5 for threestep and 6 for IRLS +# We know direct optimization is OK and direct is faster than the default d_3 fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE, error_model_algorithm = "direct") -# We know threestep is OK, and threestep (and IRLS) need 4.8 se versus 5.6 for direct +# We know threestep is OK, and threestep (and IRLS) is faster here fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE, error_model_algorithm = "threestep") diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index be2806de..101c8e15 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -2,11 +2,10 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)") # Results are from p. 40 -# Avoid warnings due to the zero value in the data for m1 at time zero -FOCUS_D <- subset(FOCUS_2006_D, value != 0) - test_that("Fits without formation fractions are correct for FOCUS D", { - fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) + expect_warning( + fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE), + "p-value.*Shapiro-Wilk") expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2), c(7.02, 23.33)) @@ -16,8 +15,7 @@ test_that("Fits without formation fractions are correct for FOCUS D", { }) test_that("Fits with formation fractions are correct for FOCUS D", { - skip_on_cran() - fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) + fit.ff <- f_sfo_sfo.ff expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), c(99.60, 0.0987, 0.0053, 0.5145)) diff --git a/tests/testthat/test_SFORB.R b/tests/testthat/test_SFORB.R index 4fb736ec..91c8f2fb 100644 --- a/tests/testthat/test_SFORB.R +++ b/tests/testthat/test_SFORB.R @@ -1,5 +1,8 @@ context("Fitting the SFORB model") +# We do not want the warnings due to non-normality of residuals here +warn_option <- options(warn=-1) + test_that("Fitting the SFORB model is equivalent to fitting DFOP", { f_sforb <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE) f_dfop <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE) @@ -32,3 +35,5 @@ test_that("Fitting the SFORB model is equivalent to fitting DFOP", { expect_equivalent(endpoints(f_sforb_sfo_eigen)$distimes, endpoints(f_dfop_sfo)$distimes, tolerance = 1e-6) }) + +options(warn = warn_option$warn) diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R index a34fa2cd..66fb1ace 100644 --- a/tests/testthat/test_analytical.R +++ b/tests/testthat/test_analytical.R @@ -1,5 +1,8 @@ context("Analytical solutions for coupled models") +# We do not want the warnings due to non-normality of residuals here +warn_option <- options(warn=-1) + test_that("The analytical solutions for SFO-SFO are correct", { # No sink, no formation fractions SFO_SFO_nosink <- mkinmod( @@ -58,3 +61,5 @@ test_that("The analytical solution for DFOP-SFO are correct", { tolerance = 5e-6 ) }) + +options(warn = warn_option$warn) diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R index 2dfb2e37..169001f1 100644 --- a/tests/testthat/test_error_models.R +++ b/tests/testthat/test_error_models.R @@ -15,36 +15,37 @@ test_that("Error model 'tc' works", { test_that("The different error model fitting methods work for parent fits", { skip_on_cran() - f_9_OLS <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, - quiet = TRUE) + test_9 <- experimental_data_for_UBA_2019[[9]]$data + + f_9_OLS <- mkinfit("SFO", test_9, quiet = TRUE) expect_equivalent(round(AIC(f_9_OLS), 2), 137.43) f_9_parms_const <- parms(f_9_OLS) - f_9_direct <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_direct <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "direct", quiet = TRUE) expect_equivalent(round(AIC(f_9_direct), 2), 134.94) f_9_parms_tc_direct <- parms(f_9_direct) - f_9_twostep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_twostep <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "twostep", quiet = TRUE) expect_equivalent(parms(f_9_twostep), f_9_parms_tc_direct, tolerance = 1e-5) - f_9_threestep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_threestep <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "threestep", quiet = TRUE) expect_equivalent(round(AIC(f_9_threestep), 2), 139.43) expect_equivalent(parms(f_9_threestep)[1:3], f_9_parms_const) - f_9_fourstep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_fourstep <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "fourstep", quiet = TRUE) expect_equivalent(round(AIC(f_9_fourstep), 2), 139.43) expect_equivalent(parms(f_9_fourstep)[1:3], f_9_parms_const) - f_9_IRLS <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_IRLS <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "IRLS", quiet = TRUE) expect_equivalent(round(AIC(f_9_IRLS), 2), 139.43) expect_equivalent(parms(f_9_IRLS)[1:3], f_9_parms_const) - f_9_d_3 <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, + f_9_d_3 <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "d_3", quiet = TRUE) expect_equivalent(round(AIC(f_9_d_3), 2), 134.94) expect_equivalent(parms(f_9_d_3), f_9_parms_tc_direct) diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index 2cc25f82..595db999 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -28,8 +28,11 @@ test_that("Test data from Appendix B are correctly evaluated", { }) test_that("Test data from Appendix D are correctly evaluated", { + # We are not interested in the warnings about non-normal residuals here + suppressWarnings( res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555", - cores = 1, quiet = TRUE) + cores = 1, quiet = TRUE) + ) # From Figure D.1 dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2) diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R index 4bff1b5a..989f963a 100644 --- a/tests/testthat/test_synthetic_data_for_UBA_2014.R +++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R @@ -7,8 +7,8 @@ test_that("Results are correct for SFO_lin_a", { M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE) - fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, - synthetic_data_for_UBA_2014[[1]]$data, + fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, + synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE) # Results for SFO_lin_a from p. 48 @@ -21,19 +21,18 @@ test_that("Results are correct for SFO_lin_a", { # Results for DFOP_par_c from p. 54 test_that("Results are correct for DFOP_par_c", { - skip_on_cran() - m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), - M1 = mkinsub("SFO"), - M2 = mkinsub("SFO"), - use_of_ff = "max", quiet = TRUE) - + skip_on_cran() - fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, - synthetic_data_for_UBA_2014[[12]]$data, - quiet = TRUE) + # Supress warning about non-normal residuals, the data were generated + # using a different error model, so no wonder + suppressWarnings( + fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, + synthetic_data_for_UBA_2014[[12]]$data, + quiet = TRUE) + ) parms <- round(fit_DFOP_par_c$bparms.optim, c(1, 4, 4, 4, 4, 4, 4, 4)) - expect_equal(parms, c(parent_0 = 103.0, + expect_equal(parms, c(parent_0 = 103.0, k_M1 = 0.0389, k_M2 = 0.0095, f_parent_to_M1 = 0.5565, f_parent_to_M2 = 0.3784, k1 = 0.3263, k2 = 0.0202, g = 0.7130)) |