add hub baseline and ensemble functions

[sbidari]

closes #4 and #5

[codecov-commenter]

Codecov Report

❌ Patch coverage is 0% with 270 lines in your changes missing coverage. Please review.
✅ Project coverage is 17.73%. Comparing base (995e858) to head (e432180).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
R/generate_hub_baselines.R	0.00%	171 Missing ⚠️
R/generate_hub_ensemble.R	0.00%	98 Missing ⚠️
R/update_hub_target_data.R	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #11       +/-   ##
===========================================
- Coverage   81.33%   17.73%   -63.61%     
===========================================
  Files           1        3        +2     
  Lines          75      344      +269     
===========================================
  Hits           61       61               
- Misses         14      283      +269     

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[Copilot]

Pull Request Overview

This PR adds functionality to generate hub baseline and ensemble forecasts for disease monitoring. The changes introduce two main functions for creating forecasts: baseline models using CDC forecasting methods and ensemble models that aggregate multiple submissions.

Key changes:

• Added baseline forecast generation using CDC baseline forecasting methods
• Added ensemble forecast generation that aggregates multiple model submissions
• Updated dependencies to include forecasting and hub-related packages

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
R/generate_hub_baselines.R	New module implementing baseline forecast generation with data latency checks
R/generate_hub_ensemble.R	New module implementing ensemble forecast creation and aggregation
R/update_hub_target_data.R	Updated to use forecasttools::write_tabular_file instead of readr::write_csv
DESCRIPTION	Added new dependencies for forecasting packages and removed readr
NAMESPACE	Exported the two new main functions
man/*.Rd	Generated documentation files for the new functions

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[sbidari]

Created #12 for adding tests

[dylanhmorris]

Looks like some of my earlier suggestions weren't applied. Did you mean to reject them @sbidari? Or has my GH just not updated?

[sbidari]

Looks like some of my earlier suggestions weren't applied. Did you mean to reject them @sbidari? Or has my GH just not updated?

I think they posted late. I am just seeing them now

[dylanhmorris]

Redo via checkmate as in the baseline function?

[dylanhmorris]

LGTM!

• A few more minor suggestions for consistency
• Not for this PR, but using the ext = argument to fs::path means that in a future PR we could make the save file format configurable to anything write_tabular supports (i.e. (csv, tsv, parquet))