Any yet more tests

5 files changed, 36 insertions, 17 deletions

diff --git a/test.log b/test.log
index 49a1a704..ddc2bc62 100644
--- a/test.log
+++ b/test.log
@@ -3,35 +3,40 @@ Loading required package: parallel
 Testing mkin
 ✔ |  OK F W S | Context
 ✔ |   5       | AIC calculation
-✔ |   2       | Export dataset for reading into CAKE [0.2 s]
-✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
+✔ |   2       | Export dataset for reading into CAKE
+✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
-✔ |   7       | Fitting the SFORB model [3.5 s]
-✔ |   5       | Analytical solutions for coupled models [3.2 s]
+✔ |   7       | Fitting the SFORB model [3.6 s]
+✔ |   5       | Analytical solutions for coupled models [3.3 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  14       | Confidence intervals and p-values [1.2 s]
-✔ |  14       | Error model fitting [4.6 s]
+✔ |  14       | Error model fitting [4.7 s]
 ✔ |   1       | Time step normalisation
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
+✔ |  23       | Nonlinear mixed effects models [8.0 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
 ✔ |   1       | mkinfit features [0.3 s]
-✔ |  12       | Special cases of mkinfit calls [0.7 s]
+✔ |  12       | Special cases of mkinfit calls [0.8 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
 ✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.6 s]
-✔ |   9       | Nonlinear mixed-effects models [7.7 s]
-✔ |  18       | Plotting [2.1 s]
+✔ |   9       | Nonlinear mixed-effects models [7.8 s]
+✖ |  15 1     | Plotting [2.0 s]
+────────────────────────────────────────────────────────────────────────────────
+FAILURE (test_plot.R:26:3): Plotting mkinfit and mmkin objects is reproducible
+Figures don't match: mmkin-plot-for-sfo-focus-c-and-d.svg
+
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |  17       | Nonlinear mixed effects models fitted with SAEM from saemix [19.1 s]
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
 ✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ |   9       | Hypothesis tests [7.4 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
+✔ |   9       | Hypothesis tests [7.3 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 62.0 s
+Duration: 50.0 s
 
-[ FAIL 0 | WARN 0 | SKIP 0 | PASS 189 ]
+[ FAIL 1 | WARN 0 | SKIP 0 | PASS 192 ]
diff --git a/tests/testthat/print_mmkin_parent.txt b/tests/testthat/print_mmkin_parent.txt
new file mode 100644
index 00000000..620a657a
--- /dev/null
+++ b/tests/testthat/print_mmkin_parent.txt
@@ -0,0 +1,13 @@
+<mmkin> object
+Status of individual fits:
+
+      dataset
+model  FOCUS_A FOCUS_C FOCUS_D
+  SFO  OK      OK      OK     
+  FOMC C       OK      OK     
+  DFOP OK      OK      OK     
+  HS   OK      OK      OK     
+
+OK: No warnings
+C: Optimisation did not converge:
+false convergence (8)
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index e3b56fb3..9da8b90d 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -35,7 +35,7 @@ f_1_mkin_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE,
 # mmkin object of parent fits for tests
 models <- c("SFO", "FOMC", "DFOP", "HS")
 fits <- mmkin(models,
-  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+  list(FOCUS_A = FOCUS_2006_A, FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
   quiet = TRUE, cores = n_cores)
 
 # One metabolite
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index 169001f1..2a1ffcc1 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -56,7 +56,6 @@ test_that("The default error model algorithm finds the best known AIC values for
   f_tc_exp_d_3 <- mmkin(c("SFO", "DFOP", "HS"),
     lapply(experimental_data_for_UBA_2019, function(x) x$data),
     error_model = "tc",
-    error_model_algorithm = "d_3",
     quiet = TRUE)
 
   AIC_exp_d_3 <- lapply(f_tc_exp_d_3, AIC)
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index ef73f21d..644cccc1 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -2,7 +2,8 @@ context("Nonlinear mixed effects models")
 
 test_that("Parent only models can be fitted using nonlinear mixed effects models", {
   # Some fits were done in the setup script
-  mmkin_sfo_2 <- mmkin("SFO", ds_sfo, fixed_initials = c(parent = 100), quiet = TRUE)
+  mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
+  expect_error(update(mmkin_sfo_1, models = c("SFOOO")), "Please supply models.*")
 
   sfo_saemix_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
   sfo_saemix_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
@@ -45,6 +46,7 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models
 })
 
 test_that("Print methods work", {
+  expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt")
   expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
   expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
   expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt")