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| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-09-12 22:16:13 +0200 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-09-12 22:16:13 +0200 |
| commit | 17af45b984d348505527140470c7fff204748ea6 (patch) | |
| tree | 4a7409236626c86e07746f7dfc736745f83a99d6 /tests | |
| parent | 3ae975f6039da0edc3ae6298bcac388e7346e73f (diff) | |
Facilitate centering covariates
The motivation for this is to obtain confidence intervals for
covariate dependent parameters that are valid for a median/mean
value of the covariate.
Implementation by adding an argument to the 'saem' function, and
adapting the relevant functions working with 'saem' objects.
Vignettes, the template and tests were updated to use the new functionality.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/testthat/test_mixed.R | 20 |
1 files changed, 20 insertions, 0 deletions
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index b9715096..99a5fd3a 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -102,15 +102,35 @@ test_that("Reading spreadsheets, finding ill-defined parameters and covariate mo error_model = "const") lambda_sforb_saem_pH <- saem(lambda_sforb, covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH)) + expect_equal( as.character(illparms(lambda_sforb_saem_pH)), c("sd(lambda_free_0)", "sd(log_k_lambda_free_bound)")) lambda_endpoints <- endpoints(lambda_sforb_saem_pH) + expect_equal(lambda_endpoints$covariates$pH, 6.45) expect_equal( round(as.numeric(lambda_endpoints$distimes), 0), c(47, 422, 127, 7, 162)) + + # We should get the same endpoints when the covariates are centered + lambda_sforb_saem_pH_centered <- saem(lambda_sforb, covariates = covariates, + covariate_models = list(log_k_lambda_bound_free ~ pH), center_covariates = "median") + lambda_endpoints_centered <- endpoints(lambda_sforb_saem_pH_centered) + + expect_equal(lambda_endpoints_centered$covariates$pH, 6.45) + expect_equal( + round(as.numeric(lambda_endpoints_centered$distimes), 0), + c(47, 422, 127, 7, 162)) + + # Also check endpoints obtained for a different pH + lambda_endpoints_centered_7 <- endpoints(lambda_sforb_saem_pH_centered, covariates = c(pH = 7)) + expect_equal(lambda_endpoints_centered_7$covariates$pH, 7) + expect_equal( + round(as.numeric(lambda_endpoints_centered_7$distimes), 0), + c(39, 283, 85, 7, 106)) + }) test_that("SFO-SFO saemix specific analytical solution work", { |