Using EpiStorm's mixing data

[gvegayon]

No description provided.

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Updates scenarios to use Epistorm-Mix contact (mixing) data and aligns the age binning to an 80plus top group.

Changes:

• Replaces POLYMOD-derived, city-specific mixing matrices with an Epistorm-Mix-based matrix saved to data/mixing_matrix.rds.
• Updates scenario documentation text to reference Epistorm-Mix instead of POLYMOD.
• Collapses census age groups from 80to84 + 85plus into a single 80plus category and updates related inputs.

Reviewed changes

Copilot reviewed 19 out of 20 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
sensitivity_analyses/references.bib	Adds a bib entry citing the Epistorm-Mix preprint.
scenarios/template.qmd	Switches mixing matrix loading logic and updates calibration call.
scenarios/Seattle.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/San Francisco.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Philadelphia.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/New York City.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Miami_hospitalizations.csv	Replaces/refreshes hospitalization input data for Miami scenario.
scenarios/Miami.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Los Angeles.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Kansas City.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Houston.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Dallas.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Boston.md	Updates narrative to say mixing is based on Epistorm-Mix.
scenarios/Atlanta.md	Updates narrative to say mixing is based on Epistorm-Mix.
data/mixing_matrix.R	Generates mixing_matrix.rds from Epistorm-Mix CSV instead of POLYMOD.
data/data	Adds a file pointing to ../data (appears to mimic a link).
data/census_age.csv	Collapses 80+ ages into a single 80plus group for each city.
data/census_age.R	Updates modeled age group boundaries to end at 80 (matching 80plus).
DETAILS.md	Notes Epistorm-Mix as the source for mixing_matrix.rds, updates POLYMOD reference.

Comments suppressed due to low confidence (1)

data/data:1

• A file named data/data containing ../data is likely unintended or a surrogate for a symlink, and it can confuse tooling and future contributors (it looks like a path pointer but is not automatically interpreted as one). If a link is required, prefer an actual symlink (if supported) or document clearly why this file is needed and how it is consumed; otherwise remove it.

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