add tests for to_epiweekly_quantile_table.R (#255)

* add test for to_epiweekly_quantiles

* move dir creation inside test_that

* review suggestions

* add tests for to_epiweekly_quantile_table

* resolve CI error

* add test to check quantiles

* Update hewr/tests/testthat/test_to_epiweekly_quantile_table.R

Co-authored-by: Damon Bayer <[email protected]>

* pre-commit changes

* fix tests error

* remove superfluous code

* use set_equal

* Update hewr/tests/testthat/test_to_epiweekly_quantile_table.R

---------

Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Damon Bayer <[email protected]>

hewr/tests/testthat/test_to_epiweekly_quantile_table.R

@@ -0,0 +1,188 @@
+create_forecast_data <- function(
+    directory, filename, date_cols, disease_cols, n_draw) {
+  data <- tidyr::expand_grid(
+    date = date_cols,
+    disease = disease_cols,
+    .draw = 1:n_draw
+  ) |>
+    dplyr::mutate(.value = sample(1:100, dplyr::n(), replace = TRUE))
+  if (length(disease_cols) == 1) {
+    data <- data |>
+      dplyr::rename(!!disease_cols := ".value") |>
+      dplyr::select(-disease)
+  }
+  arrow::write_parquet(data, fs::path(directory, filename))
+}
+
+# tests for `to_epiweekly_quantile`
+test_that("to_epiweekly_quantiles works as expected", {
+  # create temporary directories and forecast files for tests
+  temp_dir <- withr::local_tempdir("CA")
+  fs::dir_create(fs::path(temp_dir, "pyrenew_e"))
+  fs::dir_create(fs::path(temp_dir, "timeseries_e"))
+
+  create_forecast_data(
+    directory = fs::path(temp_dir, "pyrenew_e"),
+    filename = "forecast_samples.parquet",
+    date_cols = seq(
+      lubridate::ymd("2024-12-08"), lubridate::ymd("2024-12-14"),
+      by = "day"
+    ),
+    disease_cols = c("Disease", "Other", "prop_disease_ed_visits"),
+    n_draw = 20
+  )
+
+  create_forecast_data(
+    directory = fs::path(temp_dir, "timeseries_e"),
+    filename = "epiweekly_other_ed_visits_forecast.parquet",
+    date_cols = seq(
+      lubridate::ymd("2024-12-08"), lubridate::ymd("2024-12-14"),
+      by = "day"
+    ),
+    disease_cols = "other_ed_visits",
+    n_draw = 20
+  )
+
+  check_epiweekly_quantiles <- function(epiweekly_other_bool) {
+    result <- to_epiweekly_quantiles(
+      model_run_dir = temp_dir,
+      report_date = "2024-12-14",
+      max_lookback_days = 8,
+      epiweekly_other = epiweekly_other_bool
+    )
+
+    expect_s3_class(result, "tbl_df")
+    expect_setequal(c(
+      "epiweek", "epiyear", "quantile_value", "quantile_level", "location"
+    ), colnames(result))
+    expect_gt(nrow(result), 0)
+  }
+
+  check_epiweekly_quantiles(epiweekly_other_bool = FALSE)
+  check_epiweekly_quantiles(epiweekly_other_bool = TRUE)
+})
+
+
+test_that("to_epiweekly_quantiles calculates quantiles accurately", {
+  temp_dir <- withr::local_tempdir("test")
+  fs::dir_create(fs::path(temp_dir, "pyrenew_e"))
+
+  create_forecast_data(
+    directory = fs::path(temp_dir, "pyrenew_e"),
+    filename = "forecast_samples.parquet",
+    date_cols = seq(
+      lubridate::ymd("2024-12-08"), lubridate::ymd("2024-12-14"),
+      by = "day"
+    ),
+    disease_cols = c("Disease", "Other", "prop_disease_ed_visits"),
+    n_draw = 20
+  )
+
+  result <- to_epiweekly_quantiles(
+    model_run_dir = temp_dir,
+    report_date = "2024-12-14",
+    max_lookback_days = 8,
+    epiweekly_other = FALSE
+  )
+
+  forecast_path <- fs::path(
+    temp_dir,
+    "pyrenew_e",
+    "forecast_samples",
+    ext = "parquet"
+  )
+
+  quantiles <- c(0.01, 0.025, seq(0.05, 0.95, 0.05), 0.975, 0.99)
+  check_quantiles <- arrow::read_parquet(forecast_path) |>
+    dplyr::group_by(.draw, disease) |>
+    dplyr::summarise(
+      epiweekly_val = sum(.data$.value),
+      .groups = "drop"
+    ) |>
+    tidyr::pivot_wider(
+      names_from = disease,
+      values_from = epiweekly_val
+    ) |>
+    dplyr::mutate(
+      epiweekly_proportion = Disease / (Disease + Other)
+    ) |>
+    dplyr::summarise(
+      quantile_value = list(quantile(epiweekly_proportion, probs = quantiles))
+    ) |>
+    tidyr::unnest(cols = c(quantile_value)) |>
+    dplyr::mutate(
+      quantile_level = quantiles
+    )
+
+  expect_equal(
+    result$quantile_value,
+    check_quantiles$quantile_value,
+    tolerance = 1e-6
+  )
+
+  expect_equal(
+    result$quantile_level,
+    check_quantiles$quantile_level,
+    tolerance = 1e-6
+  )
+})
+
+
+test_that("to_epiweekly_quantiles handles missing forecast files", {
+  temp_dir <- withr::local_tempdir("CA")
+  fs::dir_create(fs::path(temp_dir, "pyrenew_e"))
+
+  expect_error(
+    result <- to_epiweekly_quantiles(
+      model_run_dir = temp_dir,
+      report_date = "2024-12-14",
+      max_lookback_days = 8
+    ),
+    "Failed to open local file"
+  )
+})
+
+
+# tests for `to_epiweekly_quantile_table`
+test_that("to_epiweekly_quantile_table handles multiple locations", {
+  temp_batch_dir <- withr::local_tempdir("test_model_batch_dir")
+
+  locations <- c("loc1", "loc2")
+  purrr::walk(locations, function(loc) {
+    loc_dir <- fs::path(temp_batch_dir, "model_runs", loc, "pyrenew_e")
+    fs::dir_create(loc_dir)
+
+    create_forecast_data(
+      directory = loc_dir,
+      filename = "forecast_samples.parquet",
+      date_cols = seq(
+        lubridate::ymd("2024-12-08"), lubridate::ymd("2024-12-14"),
+        by = "day"
+      ),
+      disease_cols = c("Disease", "Other", "prop_disease_ed_visits"),
+      n_draw = 20
+    )
+  })
+
+  # Rename using expected format
+  batch_dir_name <- "covid-19_r_2024-12-14_f_2024-12-08_t_2024-12-14"
+  fs::file_move(temp_batch_dir, fs::path_temp(batch_dir_name))
+  renamed_path <- fs::path_temp(batch_dir_name)
+
+  result_w_both_locations <- to_epiweekly_quantile_table(renamed_path)
+
+  expect_s3_class(result_w_both_locations, "tbl_df")
+  expect_gt(nrow(result_w_both_locations), 0)
+  expect_setequal(c(
+    "reference_date", "target", "horizon", "target_end_date",
+    "location", "output_type", "output_type_id", "value"
+  ), colnames(result_w_both_locations))
+  expect_setequal(locations, result_w_both_locations$location)
+
+  result_w_one_location <- to_epiweekly_quantile_table(
+    model_batch_dir = renamed_path,
+    exclude = "loc1"
+  )
+  expect_true("loc2" %in% result_w_one_location$location)
+  expect_false("loc1" %in% result_w_one_location$location)
+})