Add nlmixr tests, reorganize, test intervals()

1 files changed, 120 insertions, 0 deletions

diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
new file mode 100644
index 00000000..3437966f
--- /dev/null
+++ b/tests/testthat/test_dmta.R
@@ -0,0 +1,120 @@
+context("Dimethenamid data from 2018, parent fits")
+
+# Data
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
+
+# mkin
+dmta_dfop <- mmkin("DFOP", dmta_ds, quiet = TRUE)
+dmta_dfop_tc <- mmkin("DFOP", dmta_ds, error_model = "tc", quiet = TRUE)
+
+test_that("Different backends get consistent results for DFOP tc, dimethenamid data", {
+
+  # nlme
+  expect_warning(
+    nlme_dfop_tc <- nlme(dmta_dfop_tc),
+    "Iteration 3, .* false convergence")
+  ints_nlme <- intervals(nlme_dfop_tc)
+
+  # saemix
+  saem_saemix_dfop_tc <- saem(dmta_dfop_tc)
+  ints_saemix <- intervals(saem_saemix_dfop_tc)
+
+  # saemix mkin transformations
+  saem_saemix_dfop_tc_mkin <- saem(dmta_dfop_tc, transformations = "mkin")
+  ints_saemix_mkin <- intervals(saem_saemix_dfop_tc_mkin)
+
+  # nlmixr saem
+  saem_nlmixr_dfop_tc <- nlmixr(dmta_dfop_tc, est = "saem",
+    control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))
+  ints_nlmixr_saem <- intervals(saem_nlmixr_dfop_tc)
+
+  # nlmixr focei
+  # We get three warnings about nudged etas, the initial optimization and
+  # gradient problems with initial estimate and covariance
+  # We need to capture output, otherwise it pops up in testthat output
+  expect_warning(tmp <- capture_output(focei_nlmixr_dfop_tc <- nlmixr(
+      dmta_dfop_tc, est = "focei",
+      control = nlmixr::foceiControl(print = 0), all = TRUE)))
+  ints_nlmixr_focei <- intervals(focei_nlmixr_dfop_tc)
+
+  # Fixed effects
+  ## saemix vs. nlme
+  expect_true(all(ints_saemix$fixed[, "est."] >
+      backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_saemix$fixed[, "est."] <
+      backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod)))
+
+  ## saemix mkin vs. nlme
+  expect_true(all(ints_saemix_mkin$fixed[, "est."] >
+      backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_saemix_mkin$fixed[, "est."] <
+      backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod)))
+
+  ## nlmixr saem vs. nlme
+  expect_true(all(ints_nlmixr_saem$fixed[, "est."] >
+      backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_nlmixr_saem$fixed[, "est."] <
+      backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod)))
+
+  ## nlmixr focei vs. nlme
+  expect_true(all(ints_nlmixr_focei$fixed[, "est."] >
+      backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_nlmixr_focei$fixed[, "est."] <
+      backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod)))
+
+  # Random effects
+  ## for saemix with saemix transformations, the comparison would be complicated...
+  ## saemix mkin vs. nlme
+  expect_true(all(ints_saemix$random[, "est."] >
+      backtransform_odeparms(ints_nlme$reStruct$ds[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_saemix$fixed[, "est."] <
+      backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod)))
+
+  ## nlmixr saem vs. nlme
+  expect_true(all(ints_nlmixr_saem$random[, "est."] >
+      backtransform_odeparms(ints_nlme$reStruct$ds[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_nlmixr_saem$random[, "est."] <
+      backtransform_odeparms(ints_nlme$reStruct$ds[, "upper"], dmta_dfop$mkinmod)))
+
+  ## nlmixr focei vs. nlme
+  expect_true(all(ints_nlmixr_focei$random[, "est."] >
+      backtransform_odeparms(ints_nlme$reStruct$ds[, "lower"], dmta_dfop$mkinmod)))
+  expect_true(all(ints_nlmixr_focei$random[, "est."] <
+      backtransform_odeparms(ints_nlme$reStruct$ds[, "upper"], dmta_dfop$mkinmod)))
+
+  # Variance function
+  # saemix vs. nlme
+  expect_true(all(ints_saemix[[3]][, "est."] >
+      ints_nlme$varStruct[, "lower"]))
+  expect_true(all(ints_saemix[[3]][, "est."] <
+      ints_nlme$varStruct[, "upper"]))
+
+  # saemix with mkin transformations vs. nlme
+  expect_true(all(ints_saemix_mkin[[3]][, "est."] >
+      ints_nlme$varStruct[, "lower"]))
+  expect_true(all(ints_saemix_mkin[[3]][, "est."] <
+      ints_nlme$varStruct[, "upper"]))
+
+  # nlmixr saem vs. nlme
+  expect_true(all(ints_nlmixr_saem[[3]][, "est."] >
+      ints_nlme$varStruct[, "lower"]))
+  expect_true(all(ints_nlmixr_saem[[3]][, "est."] <
+      ints_nlme$varStruct[, "upper"]))
+
+  # nlmixr focei vs. nlme
+  # We only test for the proportional part (rsd_high), as the 
+  # constant part (sigma_low) obtained with nlmixr/FOCEI is below the lower
+  # bound of the confidence interval obtained with nlme
+  expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] >
+      ints_nlme$varStruct["prop", "lower"])
+  expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] <
+      ints_nlme$varStruct["prop", "upper"])
+})