testthat_bmdcalc.R
In DRomics: Dose Response for Omics

test_that("bmdcalc works as expected on the BMD results", {
  skip_on_cran()
  skip_on_os(c("mac", "linux"))
  withr::local_seed(123)
  
  datafilename <- system.file("extdata", "transcripto_sample.txt", package="DRomics")
  o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess")
  s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.001)
  f <- drcfit(s_quad, progressbar = FALSE, information.criterion = "AIC")
  
  r.1 <- bmdcalc(f, z = 1, x = 10)
  r.2 <- bmdcalc(f, z = 2, x = 50)
  BMD.zSD.1 <- r.1$res$BMD.zSD
  BMD.zSD.2 <- r.2$res$BMD.zSD
  BMD.xfold.1 <- r.1$res$BMD.xfold
  BMD.xfold.2 <- r.2$res$BMD.xfold
  
  expect_equal(sum(is.nan(BMD.zSD.1)), 0)
  expect_equal(sum(is.nan(BMD.zSD.2)), 0)
  expect_equal(sum(is.nan(BMD.xfold.1)), 1)
  expect_equal(sum(is.nan(BMD.xfold.2)), 12)
  expect_equal(sum(is.na(BMD.zSD.1)), 0)
  expect_equal(sum(is.na(BMD.zSD.2)), 5)
  expect_equal(sum(is.na(BMD.xfold.1)), 31)
  expect_equal(sum(is.na(BMD.xfold.2)), 66)
  expect_equal(round(mean(BMD.zSD.1, na.rm = TRUE), 4), 2.1107)
  expect_equal(round(mean(BMD.zSD.2, na.rm = TRUE), 4), 3.9974)
  expect_equal(round(mean(BMD.xfold.1, na.rm = TRUE), 4), 3.2778)
  expect_equal(round(mean(BMD.xfold.2, na.rm = TRUE), 4), 5.1575)
})