tests/testthat/test-ex8.r

In ABS-dev/DiagTestKit: Functions used in evaluating sensitivity and specificity at CVB Statistics

context("ex8")

test_that("values", {
  ex8_detailOut <- ex8_prevsims <- NULL
  load("./data/testdata.rda")
  ex8 <- estimateSnSp(dat = data8,
                      Sn.ref = c(ref1_result = 0.92,
                                 ref2_result = 0.88,
                                 ref3_result = 0.85),
                      Sp.ref = c(ref1_result = 0.86,
                                 ref2_result = 0.90,
                                 ref3_result = 0.92),
                      prev.pop = c(A = 0.95,
                                   B = 0.62,
                                   C = 0.18),
                      control = estimateSnSpControl(seed = 865213,
                                                    rep.iter = FALSE))
  # calcVal
  expect_equal(ex8$calcVal$Nsim,
               expected = 1000)
  expect_equal(ex8$calcVal$Confidence,
               expected = 0.95)
  expect_equal(ex8$calcVal$SnPE,
               expected = 0.965417,
               tolerance = 0.000001)
  expect_equal(ex8$calcVal$SnInterval,
               expected = round(c("5%" = 0.8879949,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)
  expect_equal(ex8$calcVal$SpPE,
               expected = 0.9835192,
               tolerance = 0.000001)
  expect_equal(ex8$calcVal$SpInterval,
               expected = round(c("5%" = 0.9016964,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)

  # detailOut
  expect_equal(ex8$detailOut$Exp.Sn,
               ex8_detailOut$Exp.Sn,
               tolerance = 0.000001)
  expect_equal(ex8$detailOut$Exp.Sp,
               ex8_detailOut$Exp.Sp,
               tolerance = 0.000001)
  expect_equal(ex8$detailOut$Converge,
               ex8_detailOut$Converge,
               tolerance = 0)
  expect_equal(ex8$detailOut$Message,
               ex8_detailOut$Message)

  # input
  expect_equal(ex8$input$seed,
               expected = 865213)
  # TODO: look at ex8$input$Sn.sims after naming fixed
  dimnames(ex8$input$prev.sims) <- NULL
  dimnames(ex8_prevsims) <- NULL
  expect_equal(ex8$input$prev.sims, ex8_prevsims)
})