Analytical solutions for all SFO variants

5 files changed, 64 insertions, 31 deletions

diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index 7284dd19..6aa73e01 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -81,7 +81,7 @@ Sum of squared residuals at call 55: 4.364078
  85.016328  -0.776316  -4.027611   1.248897 
 Sum of squared residuals at call 56: 4.364078
  85.016327  -0.776316  -4.027611   1.248897 
-Sum of squared residuals at call 57: 4.364078
+Sum of squared residuals at call 57: 4.364077
  85.016327  -0.776316  -4.027611   1.248897 
  85.016327  -0.776316  -4.027611   1.248897 
  85.008939  -0.777792  -4.026307   1.247720 
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 86d5089f..58e328cd 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -39,25 +39,27 @@ fits <- mmkin(models,
   quiet = TRUE, cores = n_cores)
 
 # One metabolite
-SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                   m1 = list(type = "SFO"),
+SFO_SFO <- mkinmod(parent = mkinsub("SFO", to = "m1"),
+                   m1 = mkinsub("SFO"),
                    use_of_ff = "min", quiet = TRUE)
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                      m1 = list(type = "SFO"),
+SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", to = "m1"),
+                      m1 = mkinsub("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")
+FOMC_SFO <- mkinmod(parent = mkinsub("FOMC", to = "m1"),
+  m1 = mkinsub("SFO"), quiet = TRUE)
 
-f_sfo_sfo_desolve <- mkinfit(SFO_SFO,
-  subset(FOCUS_2006_D, value != 0),
+# Avoid warning when fitting a dataset where zero value is removed
+FOCUS_D <- subset(FOCUS_2006_D, value != 0)
+
+f_sfo_sfo_desolve <- mkinfit(SFO_SFO, FOCUS_D,
   solution_type = "deSolve", quiet = TRUE)
-f_sfo_sfo_eigen <- mkinfit(SFO_SFO,
-  subset(FOCUS_2006_D, value != 0),
+f_sfo_sfo_eigen <- mkinfit(SFO_SFO, FOCUS_D,
   solution_type = "eigen", quiet = TRUE)
 
-f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff,
-  subset(FOCUS_2006_D, value != 0),
+f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff, FOCUS_D,
   quiet = TRUE)
 
 SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R
index 3d30e042..5972a18a 100644
--- a/tests/testthat/test_analytical.R
+++ b/tests/testthat/test_analytical.R
@@ -1,11 +1,46 @@
 context("Analytical solutions for coupled models")
 
-test_that("The analytical solution of SFO-SFO is correct", {
-  f_sfo_sfo.ff.analytical <- mkinfit(SFO_SFO.ff,
-    subset(FOCUS_2006_D, value != 0),
-    quiet = TRUE)
+test_that("The analytical solutions of SFO-SFO are correct", {
+  # No sink, no formation fractions
+  SFO_SFO_nosink <- mkinmod(
+    parent = mkinsub("SFO", to = "m1", sink = FALSE),
+    m1 = mkinsub("SFO"),
+    use_of_ff = "min", quiet = TRUE)
+  f_sfo_sfo_nosink <- mkinfit(SFO_SFO_nosink, FOCUS_D, quiet = TRUE)
+  f_sfo_sfo_nosink_deSolve <- mkinfit(SFO_SFO_nosink, FOCUS_D,
+    solution_type = "deSolve", quiet = TRUE)
+  expect_equal(
+    parms(f_sfo_sfo_nosink),
+    parms(f_sfo_sfo_nosink_deSolve)
+  )
+
+  # No sink, with formation fractions
+  SFO_SFO.ff_nosink <- mkinmod(
+    parent = mkinsub("SFO", to = "m1", sink = FALSE),
+    m1 = mkinsub("SFO"),
+    use_of_ff = "max", quiet = TRUE)
+  f_sfo_sfo_nosink <- mkinfit(SFO_SFO.ff_nosink, FOCUS_D, quiet = TRUE)
+  f_sfo_sfo_nosink_deSolve <- mkinfit(SFO_SFO.ff_nosink, FOCUS_D,
+    solution_type = "deSolve", quiet = TRUE)
+  expect_equal(
+    parms(f_sfo_sfo_nosink),
+    parms(f_sfo_sfo_nosink_deSolve)
+  )
+
+  # Without formation fraction
+  f_sfo_sfo_analytical <- mkinfit(SFO_SFO, FOCUS_D,
+    solution_type = "analytical", quiet = TRUE)
+  expect_equal(
+    parms(f_sfo_sfo_analytical),
+    parms(f_sfo_sfo_desolve)
+  )
+
+  # With formation fraction
+  f_sfo_sfo.ff_desolve <- mkinfit(SFO_SFO.ff, FOCUS_D,
+    solution_type = "deSolve", quiet = TRUE)
   expect_equal(
     parms(f_sfo_sfo.ff),
-    parms(f_sfo_sfo.ff.analytical)
+    parms(f_sfo_sfo.ff_desolve)
   )
+
 })
diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
index 002b39e2..5a66c1ef 100644
--- a/tests/testthat/test_from_max_mean.R
+++ b/tests/testthat/test_from_max_mean.R
@@ -6,15 +6,15 @@ test_that("Fitting from maximum mean value works", {
     expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, from_max_mean = TRUE),
       "only implemented for models with a single observed variable"),
     "Observations with value of zero were removed")
-  
+
   # We can either explicitly create a model for m1, or subset the data
   SFO_m1 <- mkinmod(m1 = mkinsub("SFO"))
-  f.1 <- expect_warning(mkinfit(SFO_m1, FOCUS_2006_D, from_max_mean = TRUE, quiet = TRUE))
-  expect_equivalent(endpoints(f.1)$distimes["m1", ], c(170.8, 567.5), 
-                    scale = 1, tolerance = 0.1)
+  f.1 <- mkinfit(SFO_m1, FOCUS_D, from_max_mean = TRUE, quiet = TRUE)
+  expect_equivalent(endpoints(f.1)$distimes["m1", ], c(170.8, 567.5),
+    scale = 1, tolerance = 0.1)
 
-  f.2 <- expect_warning(mkinfit("SFO", subset(FOCUS_2006_D, name == "m1"), 
-                                from_max_mean = TRUE, quiet = TRUE))
-  expect_equivalent(endpoints(f.2)$distimes["m1", ], c(170.8, 567.5), 
+  f.2 <- mkinfit("SFO", subset(FOCUS_D, name == "m1"),
+    from_max_mean = TRUE, quiet = TRUE)
+  expect_equivalent(endpoints(f.2)$distimes["m1", ], c(170.8, 567.5),
                     scale = 1, tolerance = 0.1)
 })
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
index c1e9da1d..85ee574e 100644
--- a/tests/testthat/test_mkinfit_errors.R
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -4,28 +4,24 @@ 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))
 
-  # We remove zero observations from FOCUS_2006_D beforehand in
-  # order to avoid another expect_warning in the code
-  FOCUS_2006_D <- subset(FOCUS_2006_D, value != 0)
-
   # We get a warning if we use transform_fractions = FALSE with formation fractions
   # and an error if any pathway to sink is turned off as well
   expect_warning(
     expect_error(
-      mkinfit(SFO_SFO.ff.nosink, FOCUS_2006_D, transform_fractions = FALSE, quiet = TRUE),
+      mkinfit(SFO_SFO.ff.nosink, FOCUS_D, transform_fractions = FALSE, quiet = TRUE),
       "turn off pathways to sink"
       ),
     "sum of formation fractions may exceed one")
 
-  expect_error(mkinfit(SFO_SFO.ff, FOCUS_2006_D, transform_fractions = TRUE,
+  expect_error(mkinfit(SFO_SFO.ff, FOCUS_D, transform_fractions = TRUE,
                        parms.ini = c(f_parent_to_m1 = 0.5), fixed_parms = "f_parent_to_m1", quiet = TRUE),
    "not supported")
 
-  expect_error(mkinfit(SFO_SFO.ff, FOCUS_2006_D,
+  expect_error(mkinfit(SFO_SFO.ff, FOCUS_D,
                        parms.ini = c(f_parent_to_m1 = 1.1), quiet = TRUE),
    "sum up to more than 1")
 
-  expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "analytical"), "not implemented")
+  expect_error(mkinfit(FOMC_SFO, FOCUS_D, solution_type = "analytical"), "not implemented")
 
   expect_error(mkinfit("FOMC", FOCUS_2006_A, solution_type = "eigen"), "coefficient matrix not present")
 })