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authorJohannes Ranke <jranke@uni-bremen.de>2022-02-28 14:38:23 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-02-28 14:38:23 +0100
commit37bffdcfab0ca4e0de638b1a63e808b1d29d3f15 (patch)
treec3a8ec0df74d36fcc079dd33b66457bc91b58a20 /tests/testthat/test_dmta.R
parentd68f7cc800fe2342642056780b915821dbe113e0 (diff)
Add nlmixr tests, reorganize, test intervals()
Diffstat (limited to 'tests/testthat/test_dmta.R')
-rw-r--r--tests/testthat/test_dmta.R120
1 files changed, 120 insertions, 0 deletions
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
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+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"])
+})

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