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README.md
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target_rvdss_data.csv
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README.md

Target Data for Respiratory Virus Detection Surveillance System's Lab Detections (2024-25)

Overview

The target-data folder contains the CSV data that the forecasts will be compared against. This data serves as the "gold standard" for evaluating the forecasting models. For the current Flu season, the data is stored in target-data/season_2024_2025/data_report.csv file.

Table of Contents

Lab Detections Data

Source

Respiratory Virus Detection Surveillance System (RVDSS)

Our hub's prediction targets (sarscov2_pct_positive, rsv_pct_positive and flu_pct_positive) are scraped from the Respiratory Virus Detection Surveillance System (RVDSS), published by the Public Health Agency of Canada (PHAC). The data was historically reported in weekly reports, but the current season is moved to an interactive dashboard. Historic reports and the interactive dashboard can be found here. The target data file data_reports.csv is generated using the raw data that is made available through the webscraping scripts provided by the Delphi Epi Data.

Previously collected data from earlier seasons are included in the .auxiliary-data\target-data-archive directory in their respective season sub-directories as data_reports.csv. The sarscov2_pct_positive data starts from the season_2022_2023 and hence these column values are not included in previous season data files.

Target Data Column Names (data_report.csv)

  • time_value: the last day of the epiweek

  • geo_type: the type of geographical location

  • geo_value: the actual geographical location

  • [virus]_pct_positive: the percentage of tests for a given virus that are positive (target)

Accessing Target Data

Primary Data Source: Respiratory Virus Detection Surveillance System (RVDSS)

CSV Files

A set of CSV files is updated weekly with the latest observed values for [target type, e.g., percentage of positive virus detections]. These are available at:

  • ./target-data/season_2024_2025/target_rvdss_data.csv
  • auxiliary-data/season_2024_2025_raw_files (Raw Files)

Data Processing

The rvdss_update.py code processes and updates weekly data on respiratory virus detections in Canada, automatically adding new entries. It begins by defining functions to standardize virus and geographic names (e.g., "parainfluenza" to "hpiv" and "Newfoundland" to "nl") and to categorize geographic areas (as nation, region, or province) for consistent organization.

Two main functions then retrieve and transform the data. get_revised_data() accesses historical weekly data, reformats it with a multi-index structure and ensures date consistency. get_weekly_data() retrieves data for the latest epidemiological week, determining the correct year and week from a summary file. It then applies the same formatting and standardization as with the historical data.

After processing, the code saves the data in positive_tests.csv and respiratory_detections.csv files. If these files already exist, it checks for new entries by comparing indices, appending updated data to prevent duplication. After saving updates to positive_tests.csv and respiratory_detections.csv, the code consolidates both datasets into a unified file, target_rvdss_data.csv. It includes updated geo_type values and removes duplicates, keeping only the latest (revised) entry for each combination of time_value, geo_type, and geo_value. It retains our target columns (COLUMNS_TARGET) and rounds percentage values to two decimal places, creating a ready-to-analyze file with standardized weekly data across Canada.

Source Field

For each season, the code generates three files:

  • positive_tests.csv

  • respiratory_detections.csv

    • Shows the number of positive tests for each virus (including subtypes) by week.
    • Aggregated at the lab level, with summaries at the regional level.
    • Includes revisions for each update.
    • Matches Figures 3-9 in the reports, typically titled “Positive [virus] tests (%)...”

  • target_rvdss_data.csv

    • Consolidates data from positive_tests.csv and respiratory_detections.csv.
    • Updates the geo_type field based on location corrections (from LOC_CORRECTION).
    • Removes duplicate rows, keeping only the latest (revised) entry for each combination of time_value, geo_type, and geo_value.
    • Drops unnecessary columns (e.g., issue and epiweek), creating a streamlined dataset for further analysis.

Additional Resources