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@sbidari sbidari commented Aug 21, 2025

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@sbidari sbidari changed the title Add first function to update hub format target data Add function to update hub format target data Aug 21, 2025
@sbidari sbidari requested a review from Copilot August 21, 2025 19:00

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@sbidari sbidari requested a review from dylanhmorris August 21, 2025 19:29
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Thanks @sbidari! Some suggestions and a minor but important change for the tests

@sbidari sbidari requested a review from Copilot August 22, 2025 17:31
@sbidari sbidari requested a review from dylanhmorris August 22, 2025 17:31
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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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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.

@sbidari sbidari merged commit dc18138 into main Aug 22, 2025
5 of 6 checks passed
@sbidari sbidari deleted the sb-r-package-setup branch August 22, 2025 18:23
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3 participants