diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-10-26 14:13:09 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-10-26 14:13:09 +0200 |
| commit | 0e9220c6b9132602a3d69e4be582a02da8b07822 (patch) | |
| tree | 327aed436a0bfc4df33e42f55fb2d56b04785a85 /tests/testthat | |
| parent | c615bd685d6a109306e68ea7b0516ba3d6805114 (diff) | |
Really test anova output, test covariates
Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/anova_sfo_saem.txt | 7 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 20 |
2 files changed, 22 insertions, 5 deletions
diff --git a/tests/testthat/anova_sfo_saem.txt b/tests/testthat/anova_sfo_saem.txt index e69de29b..4a21e81f 100644 --- a/tests/testthat/anova_sfo_saem.txt +++ b/tests/testthat/anova_sfo_saem.txt @@ -0,0 +1,7 @@ +Data: 262 observations of 1 variable(s) grouped in 15 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +sfo_saem_1_reduced 5 1310 1313 -650 +sfo_saem_1_reduced_mkin 5 1310 1313 -650 0 0 +sfo_saem_1 6 1312 1316 -650 0 1 1 +sfo_saem_1_mkin 6 1310 1315 -649 1 0 diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 193dcdcd..39efa18f 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -53,11 +53,21 @@ test_that("Parent fits using saemix are correctly implemented", { expect_equal(round(s_sfo_nlme_1$confint_back["k_parent", "est."], 3), round(s_sfo_saem_1$confint_back["k_parent", "est."], 3)) - # Compare fits - expect_known_output(anova(sfo_saem_1, sfo_saem_1_reduced, - sfo_saem_1_mkin, sfo_saem_1_reduced_mkin, test = TRUE), - file = "anova_sfo_saem.txt" - ) + # Compare fits with heavy rounding to avoid platform dependent results + anova_sfo <- anova( + sfo_saem_1, sfo_saem_1_reduced, + sfo_saem_1_mkin, sfo_saem_1_reduced_mkin, + test = TRUE) + anova_sfo_rounded <- round(anova_sfo, 0) + expect_known_output(print(anova_sfo_rounded), file = "anova_sfo_saem.txt") + + # Check the influence of an invented covariate + set.seed(123456) # In my first attempt I hit a false positive by chance... + pH <- data.frame(pH = runif(15, 5, 8), row.names = as.character(1:15)) + sfo_saem_pH <- update(sfo_saem_1_reduced_mkin, covariates = pH, + covariate_models = list(log_k_parent ~ pH)) + # We expect that this is not significantly better, as the covariate values were completely random + expect_true(anova(sfo_saem_1_reduced_mkin, sfo_saem_pH, test = TRUE)[2, "Pr(>Chisq)"] > 0.05) # FOMC mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) |