Test fitting without internal transformations

1 files changed, 34 insertions, 14 deletions

diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 3b241aa4..74097afa 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -19,15 +19,19 @@
 context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
 
 # Results are from p. 40
+SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                   m1 = list(type = "SFO"), quiet = TRUE)
+SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                      m1 = list(type = "SFO"),
+                      use_of_ff = "max", quiet = TRUE)
+
 
 test_that("Fits without formation fractions are correct for FOCUS D", {
-  SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                     m1 = list(type = "SFO"), quiet = TRUE)
   fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), 
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2),
                c(7.02, 23.33))
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), 
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1),
                c(131.8, 437.7))
 
   expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5),
@@ -36,20 +40,36 @@ test_that("Fits without formation fractions are correct for FOCUS D", {
 
 test_that("Fits with formation fractions are correct for FOCUS D", {
   skip_on_cran()
-  SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                        m1 = list(type = "SFO"), 
-                        use_of_ff = "max", quiet = TRUE)
-
   fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-  expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), 
+  expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)),
                     c(99.60, 0.0987, 0.0053, 0.5145))
 
-  expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), 
+  expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2),
                     c(6.40, 6.46, 4.69))
 
-  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), 
+  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2),
+               c(7.02, 23.33))
+  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1),
+               c(131.8, 437.7))
+})
+
+test_that("Fits without internal transformations are correct for FOCUS D", {
+  skip_on_cran()
+  expect_warning(
+    fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_2006_D,
+      transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE),
+    "sum of formation fractions")
+
+  expect_equivalent(round(fit.ff.notrans$bparms.optim, c(2, 4, 4, 4)),
+                    c(99.60, 0.0987, 0.0053, 0.5145))
+
+  expect_equivalent(round(100 * mkinerrmin(fit.ff.notrans)$err.min, 2),
+                    c(6.40, 6.46, 4.69))
+
+
+  expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["parent", ]), 2),
                c(7.02, 23.33))
-  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), 
+  expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["m1", ]), 1),
                c(131.8, 437.7))
 })
 
@@ -64,13 +84,13 @@ test_that("The t-value for fits using internal transformations corresponds with
                              M2 = mkinsub("SFO"),
                              use_of_ff = "min", quiet = TRUE)
 
-  fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, 
+  fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff,
                             synthetic_data_for_UBA_2014[[12]]$data,
                             quiet = TRUE)
 
   # Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test
   expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5),
-               c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588, 
+               c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588,
                  f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890,
                  k1 = 16.1450, k2 = 8.1747))
 })