tests/testthat/test-pepfar-datapack.R

In mrc-ide/naomi: Naomi Model for Subnational HIV Estimates

test_that("datapack_psnu_area_id_map is well formed", {

  psnu_map <- naomi_read_csv(system_file("datapack/datapack_psnu_area_id_map.csv"))

  expect_true(all(c("iso3", "area_id", "map_id", "map_name", "map_source") %in%
                  names(psnu_map)))
  expect_equal(anyDuplicated(psnu_map$area_id), 0)

  ## Remove _demo area_id. map_id included twice for these cases
  expect_equal(anyDuplicated(psnu_map$map_id[!grepl("_demo$", psnu_map$area_id) & !is.na(psnu_map$map_id)]), 0)

  expect_true(all(psnu_map$map_source == "Datim"))
  expect_true(all(!is.na(psnu_map$map_name[!is.na(psnu_map$map_id)])))
  expect_true(all(grepl("^[A-Z]{3}$", psnu_map$iso3)))
})

test_that("datapack_psnu_area_level is well formed", {

  psnu_level <- read_datapack_psnu()

  expect_equal(names(psnu_level), c("iso3", "psnu_area_level"))
  expect_equal(anyDuplicated(psnu_level$iso3), 0)
  expect_true(all(!is.na(psnu_level$psnu_area_level)))
  expect_type(psnu_level$psnu_area_level, "integer")
})

test_that("datapack_indicator_map is well formed", {

  datapack_indicator_map <- naomi_read_csv(system_file("datapack", "datapack_indicator_mapping.csv"))
  expect_true(all(c("indicator", "datapack_indicator_code", "is_integer", "time") %in%
                  names(datapack_indicator_map)))
  expect_true(all(datapack_indicator_map$indicator %in%
                    c(get_meta_indicator()$indicator, "circ_ever", "circ_new")))
  expect_equal(anyDuplicated(datapack_indicator_map[c("indicator", "time")]), 0)
  expect_equal(anyDuplicated(datapack_indicator_map$datapack_indicator_code), 0)
})

test_that("datapack_age_group_map is well formed", {

  datapack_age_group_map <- naomi_read_csv(system_file("datapack", "datapack_age_group_mapping.csv"))
  expect_true(all(c("age_group", "datapack_age_group_label", "datapack_age_group_id") %in%
                  names(datapack_age_group_map)))
  expect_true(all(datapack_age_group_map$age_group %in% c(get_age_groups()$age_group, "Y001_009")))
  expect_equal(anyDuplicated(datapack_age_group_map$age_group), 0)
  expect_equal(anyDuplicated(datapack_age_group_map$datapack_age_group_label), 0)
})


test_that("datapack export writes correct psnu_level", {

  tmpf <- tempfile(fileext = ".csv")
  tmpf3 <- tempfile(fileext = ".csv")
  res <- write_datapack_csv(a_output_full, tmpf)
  res3 <- write_datapack_csv(a_output_full, tmpf3, psnu_level = 3)
  expect_equal(tmpf, res)

  datapack <- readr_read_csv(res)
  datapack3 <- readr_read_csv(res3)

  expect_true(!any(is.na(datapack)))
  expect_equal(datapack, datapack3)

  ## Test level 1 data pack

  tmpf1 <- tempfile(fileext = ".csv")
  res1 <- write_datapack_csv(a_output_full, tmpf1, psnu_level = 1)
  datapack1 <- readr_read_csv(res1)

  expect_match(datapack1$area_id, "^MWI_1_")
  expect_true(!any(is.na(datapack1)))
  expect_match(datapack3$area_id, "^MWI_3_")
})

test_that("datapack export includes DMMPT2 VMMC data", {

  vmmc_path <- file.path("testdata", "vmmc.xlsx")
  vmmc_datapack_raw <- openxlsx::read.xlsx(vmmc_path, sheet = "Datapack inputs", startRow = 2)
  vmmc_datapack <- transform_dmppt2(vmmc_datapack_raw)

  tmpf <- tempfile(fileext = ".csv")
  res <- write_datapack_csv(a_output_full, tmpf, dmppt2_output = vmmc_datapack)

  datapack1 <- readr_read_csv(res)
  expect_true(!any(is.na(datapack1)))
  expect_true(all(c("VMMC_CIRC_SUBNAT.T_1", "VMMC_TOTALCIRC_SUBNAT.T_1") %in%
                    datapack1$indicator_code))
})