Improve handling of warnings, reorganize tests

8 files changed, 146 insertions, 129 deletions

diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index 9245c40b..0b31a81f 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
@@ -33,6 +33,10 @@ Fixed parameter values:
      value  type
 m1_0     0 state
 
+
+Warning(s): 
+Shapiro-Wilk test for standardized residuals: p =  0.0165
+
 Results:
 
        AIC      BIC    logLik
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
index 141f57a1..8ced5c4d 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
@@ -33,6 +33,10 @@ Fixed parameter values:
      value  type
 m1_0     0 state
 
+
+Warning(s): 
+Shapiro-Wilk test for standardized residuals: p =  0.0165
+
 Results:
 
        AIC      BIC    logLik
diff --git a/tests/testthat/test_AIC.R b/tests/testthat/test_AIC.R
new file mode 100644
index 00000000..e9698f7c
--- /dev/null
+++ b/tests/testthat/test_AIC.R
@@ -0,0 +1,12 @@
+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)
+})
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 101c8e15..0a7e5219 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -5,7 +5,7 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
 test_that("Fits without formation fractions are correct for FOCUS D", {
   expect_warning(
     fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE),
-    "p-value.*Shapiro-Wilk")
+    "Shapiro-Wilk")
 
   expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2),
                c(7.02, 23.33))
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
new file mode 100644
index 00000000..a33de07f
--- /dev/null
+++ b/tests/testthat/test_plot.R
@@ -0,0 +1,42 @@
+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)
+})
+
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)
-})
diff --git a/tests/testthat/test_summary.R b/tests/testthat/test_summary.R
new file mode 100644
index 00000000..5cf6ac6b
--- /dev/null
+++ b/tests/testthat/test_summary.R
@@ -0,0 +1,57 @@
+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$Corr <- "Correlation matrix is platform dependent, not tested"
+  expect_known_output(print(test_summary_3), "summary_DFOP_FOCUS_D_deSolve.txt")
+})
+
+test_that("A fit generated with mkin 0.9.48.1 can be summarised", {
+  # Generated with mkin 0.9.48.1
+  # SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+  #                    m1 = list(type = "SFO"), quiet = TRUE)
+  # fit_old <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+  # save(fit_old, file = "~/git/mkin/inst/testdata/fit_old_FOCUS_D.rda", version = 2 )
+  load(system.file("testdata/fit_old_FOCUS_D.rda", package = "mkin"))
+  expect_true(length(summary(fit_old)) > 0)
+})
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
new file mode 100644
index 00000000..a8fc0bd9
--- /dev/null
+++ b/tests/testthat/test_twa.R
@@ -0,0 +1,26 @@
+context("Calculation of maximum time weighted average concentrations (TWAs)")
+
+test_that("Time weighted average concentrations are correct", {
+  skip_on_cran()
+
+  outtimes_10 <- seq(0, 10, length.out = 10000)
+
+  ds <- "FOCUS_C"
+  for (model in models) {
+    fit <- fits[[model, ds]]
+    bpar <- summary(fit)$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)
+  }
+})
+