--- a +++ b/tests/testthat/test-biomarkertmle.R @@ -0,0 +1,40 @@ +library(dplyr) +library(biotmleData) +library(SuperLearner) +library(SummarizedExperiment) +data(illuminaData) + +## SETUP TESTS ################################################################ +colData(illuminaData) <- colData(illuminaData) %>% + data.frame() %>% + mutate(age = as.numeric(age > median(age))) %>% + DataFrame() +varInt_index <- which(names(colData(illuminaData)) %in% "benzene") + +biomarkerTMLEout <- biomarkertmle( + se = illuminaData[1:2, ], + varInt = varInt_index, + bppar_type = BiocParallel::SerialParam(), + g_lib = c("SL.mean", "SL.glm"), + Q_lib = c("SL.mean", "SL.glm") +) + +## BEGIN TESTS ################################################################ +test_that("biomarkertmle output object is of class type S4", { + expect_equivalent(typeof(biomarkerTMLEout), "S4") +}) + +test_that("biomarkertmle object is of appropriate custom class", { + expect_equivalent(class(biomarkerTMLEout), "bioTMLE") +}) + +test_that("biomarkertmle consistently stores input example data", { + expect_equal( + assay(biomarkerTMLEout)[1, c(17, 83, 117)], + assay(illuminaData)[1, c(17, 83, 117)], + ) +}) + +test_that("biomarkertmle output returns IC estimate for each subject", { + expect_equal(ncol(assay(biomarkerTMLEout)), ncol(illuminaData)) +})