Fix CAKE export test to actually work

Also test the model specification via the link argument

7 files changed, 18 insertions, 7 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 87823866..03346bad 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
 Version: 0.9.48.1
-Date: 2019-02-22
+Date: 2019-02-27
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 22c5f2b4..ae524e01 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2019-02-26
+Date: 2019-02-27
 Optimiser: IRLS
 
 [Data]
@@ -47,6 +47,11 @@ Time	Parent	M1
 120		33.31
 
 
+[Model]
+ParentCompartment: Parent	parent	parent
+Compartment: M1	m1	m1
+Link: Parent	M1	0.5	0	1	Free	Explicit
+
 [ComponentNames]
 Parent:parent
 M1:m1
diff --git a/tests/testthat/FOCUS_2006_D.rds b/tests/testthat/FOCUS_2006_D.rds
new file mode 100644
index 00000000..ff3b4f0f
--- /dev/null
+++ b/tests/testthat/FOCUS_2006_D.rds
diff --git a/tests/testthat/FOCUS_2006_D.txt b/tests/testthat/FOCUS_2006_D.txt
deleted file mode 100644
index e69de29b..00000000
--- a/tests/testthat/FOCUS_2006_D.txt
+++ /dev/null
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index 5f984782..23b424fc 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -22,8 +22,10 @@ test_that("Exporting is reproducible", {
   CAKE_export(list("FOCUS C" = FOCUS_2006_C,
                    "FOCUS D" = FOCUS_2006_D),
     map = c(parent = "Parent", m1 = "M1"),
+    links = c(parent = "m1"),
     filename = "FOCUS_2006_D.csf", overwrite = TRUE, 
     study = "FOCUS 2006 D")
   csf <- readLines(con = "FOCUS_2006_D.csf")
-  expect_known_output(csf, "FOCUS_2006_D.txt")
+  csf[8] <- "Date: Dummy date 0000-00-00"
+  expect_known_value(csf, file = "FOCUS_2006_D.rds")
 })
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index ff2c6f5f..42c4fcfb 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -51,9 +51,6 @@ test_that("Fits with formation fractions are correct for FOCUS D", {
                c(7.02, 23.33))
   expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1),
                c(131.8, 437.7))
-  # The following value is not from the UBA expertise, only used here
-  # to check stability of the AIC calculation
-  expect_equivalent(AIC(fit.ff), 212.6, scale = 1, tolerance = 0.1)
 })
 
 test_that("Fits without internal transformations are correct for FOCUS D", {
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 5201567d..e13111bb 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -51,7 +51,6 @@ test_that("Time weighted average concentrations are correct", {
 context("Summary")
 
 test_that("The summary is reproducible", {
-  skip_on_cran()
   fit <- fits[["DFOP", "FOCUS_C"]]
   test_summary <- summary(fit)
   test_summary$fit_version <- "Dummy 0.0 for testing"
@@ -78,3 +77,11 @@ test_that("Plotting mmkin objects is reproducible", {
   vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
 })
 
+context("AIC calculation")
+
+test_that("The AIC is reproducible", {
+  expect_equivalent(AIC(fits[["SFO", "FOCUS_C"]]), 59.8, scale = 1, tolerance = 0.1)
+  expect_equivalent(AIC(fits[, "FOCUS_C"]), 
+                    data.frame(df = c(3, 4, 5, 5), AIC = c(59.8, 44.7, 29.1, 39.3)), 
+                    scale = 1, tolerance = 0.1)
+})