Increase test coverage

6 files changed, 380 insertions, 17 deletions

diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
new file mode 100644
index 00000000..7abde0b6
--- /dev/null
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -0,0 +1,270 @@
+parent_0 log_k1 log_k2 g_ilr 
+85.1 -2.302585 -4.60517 0 
+Model cost at call  1 :  7391.39 
+85.1 -2.302585 -4.60517 0 
+85.1 -2.302585 -4.60517 0 
+Model cost at call  3 :  7391.389 
+85.1 -2.302585 -4.60517 0 
+Model cost at call  4 :  7391.389 
+85.1 -2.302585 -4.60517 1.490116e-08 
+85.06371 -1.77328 -4.250366 0.7698268 
+Model cost at call  6 :  2000.127 
+85.06375 -1.77328 -4.250366 0.7698268 
+85.06371 -1.773322 -4.250366 0.7698268 
+85.06371 -1.77328 -4.250408 0.7698268 
+85.06371 -1.77328 -4.250366 0.7697847 
+85.03542 -0.9608523 -4.11546 1.336361 
+Model cost at call  11 :  32.97798 
+85.03542 -0.9608523 -4.11546 1.336361 
+85.03542 -0.9608526 -4.11546 1.336361 
+85.03542 -0.9608523 -4.11546 1.336361 
+85.03542 -0.9608523 -4.11546 1.336361 
+85.03704 -0.256064 -4.273512 0.6447755 
+85.03285 -0.7822828 -4.127513 1.312494 
+Model cost at call  17 :  5.348133 
+85.03286 -0.7822828 -4.127513 1.312494 
+Model cost at call  18 :  5.348132 
+85.03285 -0.7822828 -4.127513 1.312494 
+Model cost at call  19 :  5.348131 
+85.03285 -0.7822828 -4.127513 1.312494 
+85.03285 -0.7822828 -4.127513 1.312494 
+Model cost at call  21 :  5.348131 
+85.02325 -0.74968 -4.059 1.14891 
+85.03127 -0.7909068 -4.114802 1.268157 
+Model cost at call  23 :  4.704445 
+85.03127 -0.7909068 -4.114802 1.268157 
+Model cost at call  24 :  4.704444 
+85.03127 -0.7909068 -4.114802 1.268157 
+85.03127 -0.7909068 -4.1148 1.268157 
+Model cost at call  26 :  4.704433 
+85.03127 -0.7909068 -4.114802 1.268158 
+85.03001 -0.7801506 -4.069435 1.262797 
+Model cost at call  28 :  4.421625 
+85.03001 -0.7801506 -4.069435 1.262797 
+85.03001 -0.7801507 -4.069435 1.262797 
+Model cost at call  30 :  4.421624 
+85.03001 -0.7801506 -4.069435 1.262797 
+85.03001 -0.7801506 -4.069435 1.262797 
+85.02878 -0.7900844 -4.023945 1.256918 
+85.02964 -0.7857352 -4.054587 1.260236 
+Model cost at call  34 :  4.414346 
+85.02964 -0.7857352 -4.054587 1.260236 
+85.02964 -0.7857351 -4.054587 1.260236 
+Model cost at call  36 :  4.414346 
+85.02964 -0.7857352 -4.054588 1.260236 
+85.02964 -0.7857352 -4.054587 1.260236 
+85.02812 -0.7778128 -4.042219 1.25389 
+Model cost at call  39 :  4.372463 
+85.02812 -0.7778128 -4.042219 1.25389 
+85.02812 -0.7778129 -4.042219 1.25389 
+Model cost at call  41 :  4.372462 
+85.02812 -0.7778128 -4.042219 1.25389 
+85.02812 -0.7778128 -4.042219 1.25389 
+85.02419 -0.7765144 -4.02942 1.245094 
+85.0263 -0.7778419 -4.036021 1.249634 
+Model cost at call  45 :  4.369313 
+85.0263 -0.7778419 -4.036021 1.249634 
+85.0263 -0.7778418 -4.036021 1.249634 
+Model cost at call  47 :  4.369313 
+85.0263 -0.7778419 -4.036022 1.249634 
+85.0263 -0.7778419 -4.036021 1.249634 
+Model cost at call  49 :  4.369313 
+85.02267 -0.7786811 -4.02967 1.252015 
+Model cost at call  50 :  4.365062 
+85.02268 -0.7786811 -4.02967 1.252015 
+85.02267 -0.7786812 -4.02967 1.252015 
+85.02267 -0.7786811 -4.02967 1.252015 
+Model cost at call  53 :  4.365062 
+85.02267 -0.7786811 -4.02967 1.252015 
+85.01633 -0.7763163 -4.027611 1.248897 
+Model cost at call  55 :  4.364078 
+85.01633 -0.7763163 -4.027611 1.248897 
+Model cost at call  56 :  4.364078 
+85.01633 -0.7763164 -4.027611 1.248897 
+Model cost at call  57 :  4.364077 
+85.01633 -0.7763163 -4.027611 1.248897 
+85.01633 -0.7763163 -4.027611 1.248897 
+85.00894 -0.7777917 -4.026307 1.24772 
+Model cost at call  60 :  4.364052 
+85.00894 -0.7777917 -4.026307 1.24772 
+Model cost at call  61 :  4.364052 
+85.00894 -0.7777917 -4.026307 1.24772 
+Model cost at call  62 :  4.364052 
+85.00894 -0.7777917 -4.026307 1.24772 
+85.00894 -0.7777917 -4.026307 1.24772 
+Model cost at call  64 :  4.364052 
+85.00518 -0.7773082 -4.026004 1.248453 
+Model cost at call  65 :  4.362751 
+85.00519 -0.7773082 -4.026004 1.248453 
+85.00518 -0.7773083 -4.026004 1.248453 
+Model cost at call  67 :  4.362751 
+85.00518 -0.7773082 -4.026005 1.248453 
+85.00518 -0.7773082 -4.026004 1.248453 
+85.00134 -0.7776046 -4.025878 1.248775 
+Model cost at call  70 :  4.362721 
+85.00135 -0.7776046 -4.025878 1.248775 
+Model cost at call  71 :  4.362721 
+85.00134 -0.7776046 -4.025878 1.248775 
+Model cost at call  72 :  4.362721 
+85.00134 -0.7776046 -4.025878 1.248775 
+85.00134 -0.7776046 -4.025878 1.248775 
+85.0032 -0.7774734 -4.0257 1.248643 
+Model cost at call  75 :  4.362715 
+85.0032 -0.7774734 -4.0257 1.248643 
+85.0032 -0.7774734 -4.0257 1.248643 
+Model cost at call  77 :  4.362715 
+85.0032 -0.7774735 -4.0257 1.248643 
+85.0032 -0.7774734 -4.0257 1.248643 
+85.0032 -0.7774734 -4.0257 1.248643 
+85.0032 -0.7774734 -4.0257 1.248643 
+85.00249 -0.7774909 -4.025911 1.248679 
+Model cost at call  82 :  4.362715 
+85.0025 -0.7774909 -4.025911 1.248679 
+Model cost at call  83 :  4.362715 
+85.00249 -0.7774909 -4.025911 1.248679 
+85.00249 -0.7774905 -4.025911 1.248679 
+85.00249 -0.7774914 -4.025911 1.248679 
+Model cost at call  86 :  4.362715 
+85.00249 -0.7774909 -4.025911 1.248679 
+85.00249 -0.7774909 -4.025911 1.248679 
+85.00249 -0.7774909 -4.025911 1.248679 
+85.00249 -0.7774909 -4.025911 1.248679 
+85.00274 -0.7774922 -4.025821 1.248672 
+Model cost at call  91 :  4.362714 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00274 -0.7774922 -4.025821 1.248672 
+Model cost at call  93 :  4.362714 
+85.00274 -0.7774921 -4.025821 1.248672 
+Model cost at call  94 :  4.362714 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00274 -0.7774922 -4.025821 1.248672 
+85.00273 -0.7774912 -4.025817 1.24867 
+Model cost at call  100 :  4.362714 
+85.00275 -0.7774912 -4.025817 1.24867 
+85.00271 -0.7774912 -4.025817 1.24867 
+85.00273 -0.7774905 -4.025817 1.24867 
+85.00273 -0.7774919 -4.025817 1.24867 
+85.00273 -0.7774912 -4.025814 1.24867 
+85.00273 -0.7774912 -4.025821 1.24867 
+85.00273 -0.7774912 -4.025817 1.248671 
+85.00273 -0.7774912 -4.025817 1.248669 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  109 :  4.362714 
+85.00276 -0.7774913 -4.025819 1.248671 
+85.00272 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774904 -4.025819 1.248671 
+85.00274 -0.7774922 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025815 1.248671 
+85.00274 -0.7774913 -4.025822 1.248671 
+85.00274 -0.7774913 -4.025819 1.248672 
+85.00274 -0.7774913 -4.025819 1.248669 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  123 :  4.362714 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+IRLS based on variance estimates according to the two component error model
+Initial variance components are:
+sigma_low  rsd_high 
+  1.08984   0.00000 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  129 :  3.673061 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  132 :  3.673061 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00273 -0.7775309 -4.025818 1.24866 
+85.00274 -0.7774953 -4.025819 1.24867 
+85.00274 -0.7774917 -4.025819 1.248671 
+85.00274 -0.7774914 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  138 :  3.673061 
+85.00277 -0.7774913 -4.025819 1.248671 
+85.0027 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774744 -4.025819 1.248671 
+85.00274 -0.7775083 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025779 1.248671 
+85.00274 -0.7774913 -4.025858 1.248671 
+85.00274 -0.7774913 -4.025819 1.248702 
+85.00274 -0.7774913 -4.025819 1.248639 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  147 :  3.673061 
+85.00276 -0.7774913 -4.025819 1.248671 
+85.00271 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774906 -4.025819 1.248671 
+85.00274 -0.7774921 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025812 1.248671 
+85.00274 -0.7774913 -4.025825 1.248671 
+85.00274 -0.7774913 -4.025819 1.248672 
+85.00274 -0.7774913 -4.025819 1.248669 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Model cost at call  159 :  3.673061 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Iteration 1 yields variance estimates:
+sigma_low  rsd_high 
+0.7434091 0.0000000 
+Sum of squared differences to last variance (component) estimates: 0.12 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00273 -0.7775366 -4.025821 1.248652 
+85.00274 -0.7774959 -4.025819 1.248669 
+85.00274 -0.7774918 -4.025819 1.24867 
+85.00274 -0.7774914 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00279 -0.7774913 -4.025819 1.248671 
+85.00268 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774621 -4.025819 1.248671 
+85.00274 -0.7775206 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025761 1.248671 
+85.00274 -0.7774913 -4.025876 1.248671 
+85.00274 -0.7774913 -4.025819 1.248714 
+85.00274 -0.7774913 -4.025819 1.248627 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00273 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774908 -4.025819 1.248671 
+85.00274 -0.7774919 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025816 1.248671 
+85.00274 -0.7774913 -4.025822 1.248671 
+85.00274 -0.7774913 -4.025819 1.248672 
+85.00274 -0.7774913 -4.025819 1.24867 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+85.00274 -0.7774913 -4.025819 1.248671 
+Iteration 2 yields variance estimates:
+sigma_low  rsd_high 
+0.7434091 0.0000000 
+Sum of squared differences to last variance (component) estimates: 2.9e-16 
+Optimisation by method Port successfully terminated.
diff --git a/tests/testthat/FOCUS_2006_C_mkinds.txt b/tests/testthat/FOCUS_2006_C_mkinds.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/tests/testthat/FOCUS_2006_C_mkinds.txt
diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
new file mode 100644
index 00000000..8e5953b9
--- /dev/null
+++ b/tests/testthat/test_from_max_mean.R
@@ -0,0 +1,17 @@
+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_error(mkinfit(SFO_SFO, FOCUS_2006_D, from_max_mean = TRUE))
+  
+  # We can either explicitly create a model for m1, or subset the data
+  SFO_m1 <- mkinmod(m1 = mkinsub("SFO"))
+  f.1 <- mkinfit(SFO_m1, FOCUS_2006_D, from_max_mean = TRUE, quiet = TRUE)
+  expect_equivalent(endpoints(f.1)$distimes["m1", ], c(170.8, 567.5), 
+                    scale = 1, tolerance = 0.1)
+
+  f.2 <- mkinfit("SFO", subset(FOCUS_2006_D, name == "m1"), from_max_mean = TRUE, quiet = TRUE)
+  expect_equivalent(endpoints(f.2)$distimes["m1", ], c(170.8, 567.5), 
+                    scale = 1, tolerance = 0.1)
+})
diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R
new file mode 100644
index 00000000..e017301c
--- /dev/null
+++ b/tests/testthat/test_mkinds.R
@@ -0,0 +1,6 @@
+context("Test dataset class mkinds used in gmkin")
+
+test_that("An mkinds object can be created and printed", {
+  testdata <- mkinds$new("FOCUS C", data = FOCUS_2006_C, time_unit = "days", unit = "%AR")
+  expect_known_output(testdata, "FOCUS_2006_C_mkinds.txt")
+})
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
new file mode 100644
index 00000000..50032628
--- /dev/null
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -0,0 +1,71 @@
+library(mkin)
+library(testthat)
+
+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))
+
+  # 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),
+      "turn off pathways to sink"
+      ),
+    "sum of formation fractions")
+
+  expect_error(mkinfit(SFO_SFO.ff, FOCUS_2006_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,
+                       parms.ini = c(f_parent_to_m1 = 1.1), quiet = TRUE),
+   "sum up to more than 1")
+
+  expect_error(mkinfit(SFO_SFO.ff, FOCUS_2006_D, solution_type = "analytical"), "not implemented")
+
+  expect_error(mkinfit("FOMC", FOCUS_2006_A, solution_type = "eigen"), "coefficient matrix not present")
+
+  # We suppress a message stemming from the interrupted call to system.time()
+  expect_error(suppressMessages(mkinfit("SFO", FOCUS_2006_A, reweight.method =
+                                        "foo", quiet = TRUE), "implemented"))
+
+})
+
+test_that("mkinfit stops early when a low maximum number of iterations is specified", {
+  expect_warning(mkinfit("SFO", FOCUS_2006_A, maxit.modFit = 1, quiet = TRUE))
+  expect_warning(mkinfit("SFO", FOCUS_2006_A, maxit.modFit = 1, quiet = TRUE, method.modFit = "Marq"))
+})
+
+test_that("mkinfit warns if the user chooses the SANN method", {
+  expect_warning(mkinfit("SFO", FOCUS_2006_A, method.modFit = "SANN", maxit.modFit = 10, quiet = TRUE))
+  skip("The SANN algorithm takes very long with the default maximum number of iterations of 10000")
+  expect_warning(mkinfit("SFO", FOCUS_2006_A, method.modFit = "SANN"))
+})
+
+test_that("mkinfit warns if a specified initial parameter value is not in the model", {
+  expect_warning(mkinfit("SFO", FOCUS_2006_A, parms.ini = c(k_xy = 0.1), quiet = TRUE))
+})
+
+test_that("We get reproducible output if quiet = FALSE", {
+  # We cannot expect parameter and sum of squares traces to be the same across platforms
+  skip_on_cran()
+  skip_on_travis()
+  expect_known_output(mkinfit("DFOP", FOCUS_2006_C, reweight.method = "tc", trace_parms = TRUE),
+    file = "DFOP_FOCUS_C_messages.txt")
+})
+
+test_that("We get warnings in case of overparameterisation", {
+  expect_warning(f <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE), "not converge")
+  s2 <- expect_warning(summary(mkinfit("DFOP", FOCUS_2006_A, quiet = TRUE)), "singular system")
+})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index e13111bb..f58ce764 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -28,23 +28,22 @@ test_that("Time weighted average concentrations are correct", {
 
   outtimes_10 <- seq(0, 10, length.out = 10000)
 
-  for (ds in c("FOCUS_C", "FOCUS_D")) {
-    for (model in models) {
-      fit <- fits[[model, ds]]
-      bpar <- summary(fit)$bpar[, "Estimate"]
-      pred_10 <- mkinpredict(fit$mkinmod,
-                  odeparms = bpar[2:length(bpar)],
-                  odeini = c(parent = bpar[[1]]),
-                  outtimes = outtimes_10)
-      twa_num <- mean(pred_10$parent)
-      names(twa_num) <- 10
-      twa_ana <- max_twa_parent(fit, 10)
-
-      # Test for absolute difference (scale = 1)
-      # The tolerance can be reduced if the length of outtimes is increased,
-      # but this needs more computing time so we stay with lenght.out = 10k
-      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
-    }
+  ds <- "FOCUS_C"
+  for (model in models) {
+    fit <- fits[[model, ds]]
+    bpar <- summary(fit)$bpar[, "Estimate"]
+    pred_10 <- mkinpredict(fit$mkinmod,
+                odeparms = bpar[2:length(bpar)],
+                odeini = c(parent = bpar[[1]]),
+                outtimes = outtimes_10)
+    twa_num <- mean(pred_10$parent)
+    names(twa_num) <- 10
+    twa_ana <- max_twa_parent(fit, 10)
+
+    # Test for absolute difference (scale = 1)
+    # The tolerance can be reduced if the length of outtimes is increased,
+    # but this needs more computing time so we stay with lenght.out = 10k
+    expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
   }
 })