Improve handling of warnings, reorganize tests

1 files changed, 0 insertions, 128 deletions

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)
-})