tests/testthat/test-bn.test.R

In jfrench/smerc: Statistical Methods for Regional Counts

data(nydf)
coords <- as.matrix(nydf[, c("x", "y")])
cases <- nydf$cases
pop <- nydf$population

bn6 <- bn.test(
  coords = coords,
  cases = cases,
  pop = pop,
  cstar = 6
)
bn12 <- bn.test(
  coords = coords,
  cases = cases,
  pop = pop,
  cstar = 12
)
bn17 <- bn.test(
  coords = coords,
  cases = cases,
  pop = pop,
  cstar = 17
)
bn23 <- bn.test(
  coords = coords,
  cases = cases,
  pop = pop,
  cstar = 23
)

context("check accuracy of bn.test")
test_that("check accuracy for bn.test for NY data", {
  expect_equal(bn6$clusters[[1]]$pop, 2921)
  expect_equal(round(bn6$clusters[[1]]$cases, 2), 8.18)

  expect_equal(bn12$clusters[[1]]$pop, 8876)
  expect_equal(round(bn12$clusters[[1]]$cases, 2), 12.21)

  expect_equal(bn17$clusters[[1]]$pop, 11268)
  expect_equal(round(bn17$clusters[[1]]$cases, 2), 17.69)

  expect_equal(bn23$clusters[[1]]$pop, 19615)
  expect_equal(round(bn23$clusters[[1]]$cases, 2), 25.46)
})

bn23mod <- bn.test(
  coords = coords,
  cases = cases,
  pop = pop,
  cstar = 23,
  modified = TRUE
)

fpath <- system.file("testdata", package = "smerc")
fname <- paste(fpath, "/bn_test_ref.rda", sep = "")
load(fname)

test_that("check accuracy for bn.test modified for NY data", {
  expect_equal(
    bn23mod$clusters[[1]]$locids,
    bnse23$clusters[[1]]$"location.IDs.included"
  )
  expect_equal(bn23mod$clusters[[1]]$pop, bnse23$clusters[[1]]$population)
  expect_equal(bn23mod$clusters[[1]]$ex, bnse23$clusters[[1]]$expected)
  expect_equal(
    bn23mod$clusters[[1]]$cases,
    bnse23$clusters[[1]]$"number.of.cases"
  )
  expect_equal(
    bn23mod$clusters[[1]]$pvalue,
    bnse23$clusters[[1]][["p.value"]]
  )

  expect_equal(
    bn23mod$clusters[[2]]$locids,
    bnse23$clusters[[2]]$"location.IDs.included"
  )
  expect_equal(bn23mod$clusters[[2]]$pop, bnse23$clusters[[2]]$population)
  expect_equal(bn23mod$clusters[[2]]$ex, bnse23$clusters[[2]]$expected)
  expect_equal(
    bn23mod$clusters[[2]]$cases,
    bnse23$clusters[[2]]$"number.of.cases"
  )
  expect_equal(
    bn23mod$clusters[[2]]$pvalue,
    bnse23$clusters[[2]][["p.value"]]
  )
})