From e6f9e9ca89e35e610d9895b979f1351a47451db0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 29 May 2020 16:05:11 +0200 Subject: Improve handling of warnings, reorganize tests --- tests/testthat/test_plots_summary_twa.R | 128 -------------------------------- 1 file changed, 128 deletions(-) delete mode 100644 tests/testthat/test_plots_summary_twa.R (limited to 'tests/testthat/test_plots_summary_twa.R') diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R deleted file mode 100644 index aedc9da3..00000000 --- a/tests/testthat/test_plots_summary_twa.R +++ /dev/null @@ -1,128 +0,0 @@ -context("Calculation of maximum time weighted average concentrations (TWAs)") - -test_that("Time weighted average concentrations are correct", { - skip_on_cran() - - outtimes_10 <- seq(0, 10, length.out = 10000) - - ds <- "FOCUS_C" - for (model in models) { - fit <- fits[[model, ds]] - bpar <- summary(fit)$bpar[, "Estimate"] - pred_10 <- mkinpredict(fit$mkinmod, - odeparms = bpar[2:length(bpar)], - odeini = c(parent = bpar[[1]]), - outtimes = outtimes_10) - twa_num <- mean(pred_10[, "parent"]) - names(twa_num) <- 10 - twa_ana <- max_twa_parent(fit, 10) - - # Test for absolute difference (scale = 1) - # The tolerance can be reduced if the length of outtimes is increased, - # but this needs more computing time so we stay with lenght.out = 10k - expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1) - } -}) - -context("Summary") - -test_that("Summaries are reproducible", { - fit <- fits[["DFOP", "FOCUS_C"]] - test_summary <- summary(fit) - test_summary$fit_version <- "Dummy 0.0 for testing" - test_summary$fit_Rversion <- "Dummy R version for testing" - test_summary$date.fit <- "Dummy date for testing" - test_summary$date.summary <- "Dummy date for testing" - test_summary$calls <- "test 0" - test_summary$Corr <- signif(test_summary$Corr, 1) - test_summary$time <- c(elapsed = "test time 0") - # The correlation matrix is quite platform dependent - # It differs between i386 and amd64 on Windows - # and between Travis and my own Linux system - test_summary$Corr <- "Correlation matrix is platform dependent, not tested" - expect_known_output(print(test_summary), "summary_DFOP_FOCUS_C.txt") - - test_summary_2 <- summary(f_sfo_sfo_eigen) - test_summary_2$fit_version <- "Dummy 0.0 for testing" - test_summary_2$fit_Rversion <- "Dummy R version for testing" - test_summary_2$date.fit <- "Dummy date for testing" - test_summary_2$date.summary <- "Dummy date for testing" - test_summary_2$calls <- "test 0" - test_summary_2$time <- c(elapsed = "test time 0") - # The correlation matrix is quite platform dependent - # It differs between i386 and amd64 on Windows - # and between Travis and my own Linux system - # Even more so when using the Eigen method - test_summary_2$Corr <- "Correlation matrix is platform dependent, not tested" - # The residuals for this method are also platform sensitive - test_summary_2$data$residual <- "not tested" - expect_known_output(print(test_summary_2), "summary_DFOP_FOCUS_D_eigen.txt") - - test_summary_3 <- summary(f_sfo_sfo_desolve) - test_summary_3$fit_version <- "Dummy 0.0 for testing" - test_summary_3$fit_Rversion <- "Dummy R version for testing" - test_summary_3$date.fit <- "Dummy date for testing" - test_summary_3$date.summary <- "Dummy date for testing" - test_summary_3$calls <- "test 0" - test_summary_3$time <- c(elapsed = "test time 0") - # The correlation matrix is quite platform dependent - # It differs between i386 and amd64 on Windows - # and between Travis and my own Linux system - test_summary_3$Corr <- "Correlation matrix is platform dependent, not tested" - expect_known_output(print(test_summary_3), "summary_DFOP_FOCUS_D_deSolve.txt") -}) - -context("Plotting") - -test_that("Plotting mkinfit and mmkin objects is reproducible", { - skip_on_cran() - plot_default_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]]) - plot_res_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]], show_residuals = TRUE) - plot_res_FOCUS_C_SFO_2 <- function() plot_res(fits[["SFO", "FOCUS_C"]]) - plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[["SFO", "FOCUS_C"]]) - mkinparplot_FOCUS_C_SFO <- function() mkinparplot(fits[["SFO", "FOCUS_C"]]) - mkinerrplot_FOCUS_C_SFO <- function() mkinerrplot(fits[["SFO", "FOCUS_C"]]) - mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"]) - mmkin_SFO <- function() plot(fits["SFO",]) - fit_D_obs_eigen <- suppressWarnings(mkinfit(SFO_SFO, FOCUS_2006_D, error_model = "obs", quiet = TRUE)) - fit_C_tc <- mkinfit("SFO", FOCUS_2006_C, error_model = "tc", quiet = TRUE) - - plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) - plot_errmod_fit_C_tc <- function() plot_err(fit_C_tc) - - plot_res_sfo_sfo <- function() plot_res(f_sfo_sfo_desolve) - plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve) - plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE) - plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE) - - skip_if(getRversion() > 4.0) - vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with defaults", plot_default_FOCUS_C_SFO) - vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with residuals like in gmkin", plot_res_FOCUS_C_SFO) - vdiffr::expect_doppelganger("plot_res for FOCUS C", plot_res_FOCUS_C_SFO_2) - vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO) - vdiffr::expect_doppelganger("mkinparplot for FOCUS C SFO", mkinparplot_FOCUS_C_SFO) - vdiffr::expect_doppelganger("mkinerrplot for FOCUS C SFO", mkinerrplot_FOCUS_C_SFO) - vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C) - vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO) - vdiffr::expect_doppelganger("plot_errmod with FOCUS C tc", plot_errmod_fit_C_tc) - skip_on_travis() # Still not working on Travis, maybe because of deSolve producing - # different results when not working with a compiled model or eigenvalues - vdiffr::expect_doppelganger("plot_errmod with FOCUS D obs eigen", plot_errmod_fit_D_obs_eigen) - vdiffr::expect_doppelganger("plot_res for FOCUS D", plot_res_sfo_sfo) - vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo) - vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_tc", plot_errmod_fit_tc_1) - vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_obs", plot_errmod_fit_obs_1) -}) - -context("AIC calculation") - -test_that("The AIC is reproducible", { - expect_equivalent(AIC(fits[["SFO", "FOCUS_C"]]), 59.3, scale = 1, tolerance = 0.1) - expect_equivalent(AIC(fits[, "FOCUS_C"]), - data.frame(df = c(3, 4, 5, 5), AIC = c(59.3, 44.7, 29.0, 39.2)), - scale = 1, tolerance = 0.1) - expect_error(AIC(fits["SFO", ]), "column object") - expect_equivalent(BIC(fits[, "FOCUS_C"]), - data.frame(df = c(3, 4, 5, 5), AIC = c(59.9, 45.5, 30.0, 40.2)), - scale = 1, tolerance = 0.1) -}) -- cgit v1.2.1