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Add function to update hub format target data #3
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Thanks @sbidari! Some suggestions and a minor but important change for the tests
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Pull Request Overview
This PR adds a new function update_hub_target_data() to retrieve and process COVID-19 and RSV target data from CDC sources for hub forecasting. The function pulls data from NHSN (hospital admissions) and NSSP (emergency department visits) datasets, formats them according to hub specifications, and saves them as parquet files.
- Adds the main
update_hub_target_data()function with support for COVID and RSV data processing - Implements comprehensive test suite with mocked API responses for both diseases
- Sets up GitHub Actions workflows for continuous integration and test coverage
Reviewed Changes
Copilot reviewed 13 out of 16 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| R/update_hub_target_data.R | Core function implementation for data retrieval and processing |
| tests/testthat/test_update_hub_target_data.R | Test suite with mocked API calls for both COVID and RSV scenarios |
| tests/testthat/setup.R | Test configuration for httptest2 mocking |
| tests/testthat/api_mocks/*.json | Mock API response data for testing |
| man/update_hub_target_data.Rd | Documentation for the new function |
| DESCRIPTION | Updated dependencies and remotes |
| .github/workflows/*.yaml | CI/CD workflows for R package checks and coverage |
Comments suppressed due to low confidence (1)
DESCRIPTION:25
- The Config/testthat/edition line appears to be removed but should be retained to specify testthat edition 3, which is important for test configuration.
httptest2,
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dylanhmorris
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LGTM! Minor suggestions you can take or leave. Would be good to have tests for some of the configurable options, but I will leave to you whether to do that here or in a separate PR.
Co-authored-by: Dylan H. Morris <[email protected]>
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