Reorganize tests to reduce time on winbuilder

9 files changed, 52 insertions, 62 deletions

diff --git a/test.log b/test.log
index 7b397ee1..4ae27f0d 100644
--- a/test.log
+++ b/test.log
@@ -1,16 +1,15 @@
 Loading mkin
 Testing mkin
-Successfully compiled differential equation model from auto-generated C code.
 ✔ |  OK F W S | Context
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  10       | Confidence intervals and p-values [10.2 s]
-✔ |  10       | Error model fitting [38.3 s]
-✔ |   5       | Calculation of FOCUS chi2 error levels [3.5 s]
-✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s]
-✔ |   6       | Test fitting the decline of metabolites from their maximum [0.9 s]
+✔ |  10       | Confidence intervals and p-values [9.7 s]
+✔ |  10       | Error model fitting [37.4 s]
+✔ |   4       | Calculation of FOCUS chi2 error levels [2.2 s]
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.4 s]
+✔ |   6       | Test fitting the decline of metabolites from their maximum [0.7 s]
 ✔ |   1       | Fitting the logistic model [0.9 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |  12       | Special cases of mkinfit calls [2.7 s]
+✔ |  12       | Special cases of mkinfit calls [2.4 s]
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
 ✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
@@ -22,11 +21,11 @@ Successfully compiled differential equation model from auto-generated C code.
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
 ✔ |   4       | Fitting the SFORB model [1.7 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
-✔ |   5       | Hypothesis tests [9.9 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
+✔ |   6       | Hypothesis tests [31.3 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 91.5 s
+Duration: 109.7 s
 
 OK:       127
 Failed:   0
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index fc972a3d..9becdd2a 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -47,6 +47,9 @@ SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
 SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
                       m1 = list(type = "SFO"),
                       use_of_ff = "max", quiet = TRUE)
+SFO_SFO.ff.nosink <- mkinmod(
+  parent = mkinsub("SFO", "m1", sink = FALSE),
+  m1 = mkinsub("SFO"), quiet = TRUE, use_of_ff = "max")
 
 f_sfo_sfo_desolve <- mkinfit(SFO_SFO,
   subset(FOCUS_2006_D, value != 0),
@@ -76,8 +79,6 @@ m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
   use_of_ff = "max", quiet = TRUE)
 
 fit_nw_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
-fit_nw_1_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
-  error_model = "const", error_model_algorithm = "direct")
 
 # We know direct optimization is OK and direct needs 4 sec versus 5.5 for threestep and 6 for IRLS
 fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE,
@@ -85,19 +86,3 @@ fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TR
 # We know threestep is OK, and threestep (and IRLS) need 4.8 se versus 5.6 for direct
 fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE,
   error_model_algorithm = "threestep")
-
-# We know direct optimization is OK and direct needs 8 sec versus 11 sec for threestep
-f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
-  error_model_algorithm = "direct", quiet = TRUE)
-
-# Experimental data for UBA
-dfop_sfo_sfo <- mkinmod(
-  parent = mkinsub("DFOP", to = "A1"),
-  A1 = mkinsub("SFO", to = "A2"),
-  A2 = mkinsub("SFO"),
-  use_of_ff = "max"
-)
-
-f_soil_1_tc <- mkinfit(dfop_sfo_sfo,
-  experimental_data_for_UBA_2019[[1]]$data,
-  error_model = "tc", quiet = TRUE)
diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R
index d7f8d9e7..d091cb95 100644
--- a/tests/testthat/test_FOCUS_chi2_error_level.R
+++ b/tests/testthat/test_FOCUS_chi2_error_level.R
@@ -18,10 +18,6 @@
 
 context("Calculation of FOCUS chi2 error levels")
 
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                      m1 = list(type = "SFO"),
-                      use_of_ff = "max", quiet = TRUE)
-
 errmin.FOCUS_2006_D_rounded = data.frame(
   err.min = c(0.0640, 0.0646, 0.0469),
   n.optim = c(4, 2, 2),
@@ -36,16 +32,13 @@ errmin.FOCUS_2006_E_rounded = data.frame(
 
 test_that("Chi2 error levels for FOCUS D are as in mkin 0.9-33", {
 
-  fit <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE),
-                        "Observations with value of zero")
-
-
-  expect_equal(round(mkinerrmin(fit), 4),
+  expect_equal(round(mkinerrmin(f_sfo_sfo.ff), 4),
                errmin.FOCUS_2006_D_rounded)
 })
 
 test_that("Chi2 error levels are independent of setting parms.ini that are not in the model", {
 
+  skip_on_cran()
   fit.2 <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE,
                                 parms.ini = c(tb = 5)),
                         "Observations with value of zero")
diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R
index 2443fa66..a2bf1401 100644
--- a/tests/testthat/test_confidence.R
+++ b/tests/testthat/test_confidence.R
@@ -73,7 +73,8 @@ test_that("Likelihood profile based confidence intervals work", {
    }
    f_mle <- stats4::mle(f_nll, start = as.list(parms(f)), nobs = nrow(FOCUS_2006_C))
 
-   ci_mkin_1_p_0.95 <- confint(f, method = "profile", level = 0.95, quiet = TRUE)
+   ci_mkin_1_p_0.95 <- confint(f, method = "profile", level = 0.95, 
+     cores = n_cores, quiet = TRUE)
 
    # Magically, we get very similar boundaries as stats4::mle
    # (we need to capture the output to avoid printing this while testing as
diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
index c4d6bfe4..3edf5969 100644
--- a/tests/testthat/test_from_max_mean.R
+++ b/tests/testthat/test_from_max_mean.R
@@ -19,8 +19,7 @@
 context("Test fitting the decline of metabolites from their maximum")
 
 test_that("Fitting from maximum mean value works", {
-  SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"),
-                     m1 = mkinsub("SFO"))
+
   expect_warning(
     expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, from_max_mean = TRUE),
       "only implemented for models with a single observed variable"),
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
index 8adb05c1..3a04e9c6 100644
--- a/tests/testthat/test_mkinfit_errors.R
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -18,14 +18,6 @@
 
 context("Special cases of mkinfit calls")
 
-SFO_SFO.ff.nosink <- mkinmod(
-  parent = mkinsub("SFO", "m1", sink = FALSE),
-  m1 = mkinsub("SFO"), quiet = TRUE, use_of_ff = "max")
-
-SFO_SFO.ff <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"), quiet = TRUE, use_of_ff = "max")
-
 test_that("mkinfit stops to prevent and/or explain user errors", {
   expect_error(mkinfit("foo", FOCUS_2006_A))
   expect_error(mkinfit(3, FOCUS_2006_A))
diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
index 3fcdb3a2..d0d856fa 100644
--- a/tests/testthat/test_mkinpredict_SFO_SFO.R
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -31,20 +31,20 @@ test_that("Variants of model predictions for SFO_SFO model give equivalent resul
          m1 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE)

 

   ot = seq(0, 100, by = 1)

-  r.1.e <- subset(mkinpredict(SFO_SFO.1, 

-             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

-             c(parent = 100, m1 = 0), ot, solution_type = "eigen"), 

+  r.1.e <- subset(mkinpredict(SFO_SFO.1,

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1),

+             c(parent = 100, m1 = 0), ot, solution_type = "eigen"),

                  time %in% c(1, 10, 50, 100))

-  r.1.d <- subset(mkinpredict(SFO_SFO.1, 

-             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

-             c(parent = 100, m1 = 0), ot, solution_type = "deSolve"), 

+  r.1.d <- subset(mkinpredict(SFO_SFO.1,

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1),

+             c(parent = 100, m1 = 0), ot, solution_type = "deSolve"),

                  time %in% c(1, 10, 50, 100))

 

-  r.2.e <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

-	    c(parent = 100, m1 = 0), ot, solution_type = "eigen"),

+  r.2.e <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1),

+      c(parent = 100, m1 = 0), ot, solution_type = "eigen"),

                   time %in% c(1, 10, 50, 100))

-  r.2.d <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

-	    c(parent = 100, m1 = 0), ot, solution_type = "deSolve"),

+  r.2.d <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1),

+      c(parent = 100, m1 = 0), ot, solution_type = "deSolve"),

                   time %in% c(1, 10, 50, 100))

 

   # Compare eigen and deSolve for minimum use of formation fractions

diff --git a/tests/testthat/test_residuals.R b/tests/testthat/test_residuals.R
index 275b33b9..35a143f6 100644
--- a/tests/testthat/test_residuals.R
+++ b/tests/testthat/test_residuals.R
@@ -4,5 +4,7 @@ test_that("Residuals are correctly returned", {
   f <- fits[["FOMC", "FOCUS_C"]]
   expect_equal(residuals(f)[1:3], c(-0.7748906, 2.7090589, -1.9451989))
 
-  expect_equivalent(residuals(f_tc_2, standardized = TRUE)[1:3], c(0.52579103, 0.40714911, 1.66394233), tolerance = 0.0001)
+  expect_equivalent(
+    residuals(f, standardized = TRUE)[1:3],
+    c(-0.4171812, 1.4584875, -1.0472450), tolerance = 0.0001)
 })
diff --git a/tests/testthat/test_tests.R b/tests/testthat/test_tests.R
index d8b97815..6edb4dfa 100644
--- a/tests/testthat/test_tests.R
+++ b/tests/testthat/test_tests.R
@@ -2,7 +2,7 @@ context("Hypothesis tests")
 
 test_that("The likelihood ratio test works", {
 
-  expect_error(lrtest(fit_tc_1, f_tc_2), "not been fitted to the same data")
+  expect_error(lrtest(f_1_mkin_trans, f_2_mkin), "not been fitted to the same data")
 
   res <- lrtest(fit_nw_1, fit_tc_1)
   expect_equal(res[["2", "Pr(>Chisq)"]], 1, tolerance = 1e-5)
@@ -10,13 +10,27 @@ test_that("The likelihood ratio test works", {
 })
 
 test_that("We can conveniently fix parameters using 'fixed_parms'", {
+
   f_k2_fixed <- mkinfit("DFOP", FOCUS_2006_C, fixed_parms = c(k2 = 0.05), quiet = TRUE)
   expect_equivalent(f_k2_fixed$bparms.ode["k2"], 0.05)
+
 })
 
 test_that("Updating fitted models works", {
-  f_dfop_const <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
-  f_dfop_tc <- update(f_dfop_const, error_model = "tc")
+
+  skip_on_cran()
+  f_dfop_tc <- update(f_2_mkin, error_model = "tc")
+
+  dfop_sfo_sfo <- mkinmod(
+    parent = mkinsub("DFOP", to = "A1"),
+    A1 = mkinsub("SFO", to = "A2"),
+    A2 = mkinsub("SFO"),
+    use_of_ff = "max"
+  )
+
+  f_soil_1_tc <- mkinfit(dfop_sfo_sfo,
+    experimental_data_for_UBA_2019[[1]]$data,
+    error_model = "tc", quiet = TRUE)
 
   f_soil_1_nw <- update(f_soil_1_tc, error_model = "const")
   f_soil_1_nw_A2 <- update(f_soil_1_nw, fixed_parms = c(k_A2 = 0))
@@ -25,3 +39,8 @@ test_that("Updating fitted models works", {
   test_nw_A2 <- lrtest(f_soil_1_nw, f_soil_1_nw_A2)
   expect_equivalent(test_nw_A2[["2", "Pr(>Chisq)"]], 1, tolerance = 1e-4)
 })
+
+test_that("We can do a likelihood ratio test using an update specification", {
+  test_2_mkin_k2 <- lrtest(f_2_mkin, fixed_parms = c(k2 = 0))
+  expect_equivalent(test_2_mkin_k2[["2", "Pr(>Chisq)"]], 1.139e-6, tolerance = 1e-8)
+})