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create_tidy_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)) | ||
} | ||
|
||
create_observation_data <- function( | ||
date_cols, location_cols) { | ||
data <- tidyr::expand_grid( | ||
reference_date = date_cols, | ||
location = location_cols | ||
) |> | ||
dplyr::mutate(value = sample(1:100, dplyr::n(), replace = TRUE)) | ||
return(data) | ||
} | ||
|
||
create_hubverse_table <- function( | ||
date_cols, horizon, location, output_type, output_type_id) { | ||
data <- tidyr::expand_grid( | ||
reference_date = date_cols, | ||
horizon = horizon, | ||
output_type_id = output_type_id, | ||
location = location | ||
) |> | ||
dplyr::group_by(reference_date, horizon, location) |> | ||
dplyr::mutate( | ||
value = sort( | ||
sample(1:100, dplyr::n(), replace = TRUE), | ||
decreasing = FALSE | ||
), | ||
target = "wk inc covid prop ed visits", | ||
output_type = "quantile", | ||
target_end_date = reference_date + 7 * horizon | ||
) |> | ||
dplyr::ungroup() | ||
|
||
return(data) | ||
} |
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testthat::test_that("score_hubverse works as expected with valid inputs", { | ||
forecast <- create_hubverse_table( | ||
date_cols = seq( | ||
lubridate::ymd("2023-11-01"), lubridate::ymd("2024-01-29"), | ||
by = "day" | ||
), | ||
horizon = c(0, 1, 2), | ||
location = c("loc1", "loc2"), | ||
output_type = "quantile", | ||
output_type_id = c(0.01, 0.025, seq(0.05, 0.95, 0.05), 0.975, 0.99) | ||
) | ||
|
||
observed <- create_observation_data( | ||
date_cols = seq( | ||
lubridate::ymd("2023-11-01"), lubridate::ymd("2024-01-29"), | ||
by = "day" | ||
), | ||
location = c("loc1", "loc2") | ||
) | ||
|
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scored <- score_hubverse(forecast, observed) | ||
expect_setequal(forecast$location, scored$location) | ||
expect_setequal(scored$horizon, c(0, 1)) | ||
|
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scored_all_horizon <- score_hubverse( | ||
forecast, observed, | ||
horizons = c(0, 1, 2) | ||
) | ||
expect_setequal(forecast$location, scored_all_horizon$location) | ||
expect_setequal(forecast$horizon, scored_all_horizon$horizon) | ||
}) | ||
|
||
|
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testthat::test_that("score_hubverse handles missing location data", { | ||
forecast <- create_hubverse_table( | ||
date_cols = seq( | ||
lubridate::ymd("2024-11-01"), lubridate::ymd("2024-11-29"), | ||
by = "day" | ||
), | ||
horizon = c(0, 1), | ||
location = c("loc1", "loc2"), | ||
output_type = "quantile", | ||
output_type_id = seq(0.05, 0.95, 0.05) | ||
) | ||
|
||
observed <- create_observation_data( | ||
date_cols = seq( | ||
lubridate::ymd("2024-11-01"), lubridate::ymd("2024-11-29"), | ||
by = "day" | ||
), | ||
location = c("loc1") | ||
) | ||
|
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result <- score_hubverse(forecast, observed) | ||
expect_false("loc2" %in% result$location) | ||
expect_setequal(observed$location, result$location) | ||
}) | ||
|
||
|
||
testthat::test_that("score_hubverse handles zero length forecast table", { | ||
forecast <- tibble::tibble( | ||
reference_date = as.Date(character(0)), | ||
horizon = integer(0), | ||
output_type_id = numeric(0), | ||
location = character(0), | ||
value = numeric(0), | ||
target = character(0), | ||
output_type = character(0), | ||
target_end_date = as.Date(character(0)) | ||
) | ||
|
||
observed <- create_observation_data( | ||
date_cols = seq( | ||
lubridate::ymd("2024-11-01"), lubridate::ymd("2024-11-02"), | ||
by = "day" | ||
), | ||
location = c("loc1") | ||
) | ||
|
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expect_error( | ||
result <- score_hubverse(forecast, observed), | ||
"Assertion on 'data' failed: Must have at least 1 rows, but has 0 rows." | ||
) | ||
}) |
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# Pipelines |
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