add a test

Author: sbidari

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(hubhelpr)
+
+test_check("hubhelpr")

tests/testthat/test_update_hub_target_data.R

@@ -0,0 +1,114 @@
+library(fs)
+library(dplyr)
+library(testthat)
+library(hubhelpr)
+library(forecasttools)
+
+run_update_hub_target_data_test <- function(
+  disease,
+  nhsn_col,
+  nssp_col,
+  nhsn_target,
+  nssp_target
+) {
+  base_hub_path <- tempfile(paste0("base_hub_", disease, "_"))
+  dir_create(base_hub_path)
+  output_file <- path(base_hub_path, "target-data/time-series.parquet")
+  fs::dir_create(fs::path(base_hub_path, "target-data"))
+
+  mock_target_ts <- tibble::tibble(
+    date = as.Date(character()),
+    observation = numeric(),
+    location = character(),
+    as_of = as.Date(character()),
+    target = character()
+  )
+  forecasttools::write_tabular_file(mock_target_ts, output_file)
+
+  mock_nhsn <- tibble::tibble(
+    weekendingdate = as.Date(c(
+      "2024-11-09",
+      "2024-11-16",
+      "2024-11-09",
+      "2024-11-16"
+    )),
+    jurisdiction = c("MI", "MI", "CA", "CA"),
+    totalconfc19newadm = c(1, 2, 1, 0),
+    totalconfrsvnewadm = c(3, 4, 3, 2)
+  )
+  mock_nssp <- tibble::tibble(
+    week_end = as.Date(c("2024-11-09", "2024-11-09")),
+    county = c("All", "All"),
+    geography = c("Alabama", "Alaska"),
+    percent_visits_covid = c(1.0, 0.2),
+    percent_visits_rsv = c(0.5, 0.15)
+  )
+  assignInNamespace(
+    "pull_data_cdc_gov_dataset",
+    function(dataset, columns, start_date = NULL, locations = NULL) {
+      if (dataset == "nhsn_hrd_prelim") {
+        mock_nhsn |>
+          dplyr::select(weekendingdate, jurisdiction, all_of(columns))
+      } else if (dataset == "nssp_prop_ed_visits") {
+        mock_nssp |> dplyr::select(week_end, geography, all_of(columns))
+      } else {
+        stop("Unknown dataset")
+      }
+    },
+    ns = "forecasttools"
+  )
+
+  expect_silent(
+    update_hub_target_data(
+      base_hub_path = base_hub_path,
+      disease = disease,
+      first_full_weekending_date = as.Date("2024-11-09")
+    )
+  )
+
+  target_ts <- forecasttools::read_tabular_file(output_file)
+
+  expect_true(all(
+    c("date", "observation", "location", "as_of", "target") %in%
+      names(target_ts)
+  ))
+
+  expect_equal(
+    target_ts |>
+      dplyr::select(date, observation, location, target) |>
+      dplyr::arrange(date, location),
+    tibble::tibble(
+      date = as.Date(c(mock_nhsn$weekendingdate, mock_nssp$week_end)),
+      observation = c(
+        as.numeric(mock_nhsn[[nhsn_col]]),
+        as.numeric(mock_nssp[[nssp_col]]) / 100
+      ),
+      location = c(
+        us_location_recode(mock_nhsn$jurisdiction, "abbr", "code"),
+        us_location_recode(mock_nssp$geography, "name", "code")
+      ),
+      target = c(rep(nhsn_target, 4), rep(nssp_target, 2))
+    ) |>
+      dplyr::arrange(date, location)
+  )
+}
+
+test_that("update_hub_target_data returns exactly the mocked NHSN data for covid", {
+  run_update_hub_target_data_test(
+    disease = "covid",
+    nhsn_col = "totalconfc19newadm",
+    nssp_col = "percent_visits_covid",
+    nhsn_target = "wk inc covid hosp",
+    nssp_target = "wk inc covid prop ed visits"
+  )
+})
+
+test_that("update_hub_target_data returns exactly the mocked NHSN data for rsv", {
+  run_update_hub_target_data_test(
+    disease = "rsv",
+    nhsn_col = "totalconfrsvnewadm",
+    nssp_col = "percent_visits_rsv",
+    nhsn_target = "wk inc rsv hosp",
+    nssp_target = "wk inc rsv prop ed visits"
+  )
+})