tests/testthat/test_handling.R

In Hackout3/epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts

context("Handling: [ operator")

test_that("Various subsetting using [", {
  
  ## Add list elements for testing
  linelist <- ebola_sim$linelist
  linelist$latlon <- replicate(nrow(linelist),
                               runif(2, -90, 90),
                               simplify = FALSE)

  x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
                        id = "case_id", to = "case_id", from = "infector",
                        directed = TRUE)

  ## make subsets
  x0 <- x["toto", "tata"]
  x1 <- x[get_id(x, "linelist")[1:10]]
  x2 <- x[j = get_id(x, "contacts")[1:10], contacts = "either"]
  x3 <- x[j = get_id(x, "contacts")[1:10], contacts = "both"]
  x4 <- x[j = get_id(x, "from")[1:3], contacts="from"]
  x5 <- x[j = get_id(x, "to")[1:3], contacts="to"]
  x6 <- x[1:3, 1:3, k = 2:1, l = 1]
  x7 <- x[k = FALSE, l = FALSE]

  expect_is(x0, "epicontacts")
  expect_is(x1, "epicontacts")
  expect_is(x2, "epicontacts")
  expect_is(x3, "epicontacts")
  expect_is(x4, "epicontacts")
  expect_is(x5, "epicontacts")
  expect_is(x6, "epicontacts")
  expect_is(x7, "epicontacts")

  expect_equal(nrow(x0$linelist), 0)
  expect_equal(nrow(x0$contacts), 0)

  expect_equal(nrow(x2$linelist), nrow(x$linelist))
  expect_equal(nrow(x2$contacts), 16)

  expect_equal(nrow(x3$linelist), nrow(x$linelist))
  expect_true(all(get_id(x3, "contacts") %in% get_id(x, "contacts")[1:10]))
  expect_equal(nrow(x3$contacts), 3)

  expect_equal(nrow(x4$linelist), nrow(x$linelist))
  expect_true(all(get_id(x4, "from") %in% get_id(x, "from")[1:3]))
  expect_equal(nrow(x4$contacts), 4)

  expect_equal(nrow(x5$linelist), nrow(x$linelist))
  expect_true(all(get_id(x5, "to") %in% get_id(x, "to")[1:3]))
  expect_equal(nrow(x5$contacts), 3)

  expect_equal(dim(x6$linelist), c(3,3))
  expect_equal(dim(x6$contacts), c(3,3))
  expect_identical(names(x6$linelist), names(x$linelist)[c(1,3,2)])

  expect_equal(dim(x7$linelist), c(nrow(x$linelist), 1))
  expect_equal(dim(x7$contacts), c(nrow(x$contacts), 2))

})

test_that("Errors / warnings happen when they should", {
  x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
                        id = "case_id", to = "case_id", from = "infector",
                        directed = FALSE)

  expect_error(x[j = get_id(x)[1:100], contacts="tamere"],
               ".*should be one of.*")
})