tests/testthat/test-ex5.r

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

context("ex5")

test_that("values", {
  ex5_detailOut <- ex5_prevsims <- NULL
  load("./data/testdata.rda")
  ex5 <- estimateSnSp(dat = data5,
                      Sn.ref = c(Ref1 = 0.90),
                      Sp.ref = c(Ref1 = 0.99),
                      prev.pop = c(A = 0.80,
                                   B = 0.90),
                      control = estimateSnSpControl(seed = 1249856,
                                                    rep.iter = FALSE))
  # calcVal
  expect_equal(ex5$calcVal$Nsim,
               expected = 1000)
  expect_equal(ex5$calcVal$Confidence,
               expected = 0.95)
  expect_equal(ex5$calcVal$SnPE,
               expected = 0.9412681,
               tolerance = 0.000001)
  expect_equal(ex5$calcVal$SnInterval,
               expected = round(c("5%" = 0.8937435,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)
  expect_equal(ex5$calcVal$SpPE,
               expected = 0.8721353,
               tolerance = 0.000001)
  expect_equal(ex5$calcVal$SpInterval,
               expected = round(c("5%" = 0.7169586,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)

  # detailOut
  expect_equal(ex5$detailOut$Exp.Sn,
               ex5_detailOut$Exp.Sn,
               tolerance = 0.000001)
  expect_equal(ex5$detailOut$Exp.Sp,
               ex5_detailOut$Exp.Sp,
               tolerance = 0.000001)
  expect_equal(ex5$detailOut$Converge,
               ex5_detailOut$Converge,
               tolerance = 0)
  expect_equal(ex5$detailOut$Message,
               ex5_detailOut$Message)

  # input
  expect_equal(ex5$input$seed,
               expected = 1249856)
  # TODO: look at ex5$input$Sn.sims after naming fixed

  dimnames(ex5$input$prev.sims) <- NULL
  dimnames(ex5_prevsims) <- NULL
  expect_equal(ex5$input$prev.sims,
               ex5_prevsims)
})