tests/testthat/test-ex7.r

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

context("ex7")
test_that("values", {
  ex7_detailOut <- ex7_prevsims <- NULL
  load("./data/testdata.rda")
  ex7 <- estimateSnSp(dat = data7,
                      Sn.ref = data.frame(ref1 = c(0.88, 0.75),
                                          ref2 = c(0.90, 0.55)),
                      Sp.ref = data.frame(ref1 = c(0.97, 0.6),
                                          ref2 = c(0.95, 0.5)),
                      prev.pop = c(A = 0.87,
                                   B = 0.35),
                      control = estimateSnSpControl(seed = 1937457,
                                                    rep.iter = FALSE))

  # calcVal
  expect_equal(ex7$calcVal$Nsim,
               expected = 1000)
  expect_equal(ex7$calcVal$Confidence,
               expected = 0.95)
  expect_equal(ex7$calcVal$SnPE,
               expected = 0.966133,
               tolerance = 0.000001)
  expect_equal(ex7$calcVal$SnInterval,
               expected = round(c("5%" = 0.9157368,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)
  expect_equal(ex7$calcVal$SpPE,
               expected = 0.9215106,
               tolerance = 0.000001)
  expect_equal(ex7$calcVal$SpInterval,
               expected = round(c("5%" = 0.8715217,
                                  "100%" = 1),
                                digits = 7),
               tolerance = 0.000001)

  # detailOut
  expect_equal(ex7$detailOut$Exp.Sn,
               ex7_detailOut$Exp.Sn,
               tolerance = 0.000001)
  expect_equal(ex7$detailOut$Exp.Sp,
               ex7_detailOut$Exp.Sp,
               tolerance = 0.000001)
  expect_equal(ex7$detailOut$Converge,
               ex7_detailOut$Converge,
               tolerance = 0)
  expect_equal(ex7$detailOut$Message,
               ex7_detailOut$Message)

  # input
  expect_equal(ex7$input$seed,
               expected = 1937457)
  # TODO: look at ex7$input$Sn.sims after naming fixed
  dimnames(ex7$input$prev.sims) <- NULL
  dimnames(ex7_prevsims) <- NULL
  expect_equal(ex7$input$prev.sims,
               ex7_prevsims)
})