A Guide to Accounting for Reporting Delays in State, Local, and Territorial Public Health Surveillance Data

A practical guide for epidemiologists, public health practitioners, and modellers working with delayed surveillance data.

Abstract

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Links

📖 Read the paper (PDF)

🌐 Read the paper (HTML)

🌐 Guidance website (interactive decision tree and guidance)

💻 User-submitted snippets (community code examples)

💻 Source Code (GitHub)

Output plan

Primary output

• Manuscript (preprint, then journal submission)

Secondary outputs

• Website version of content (coordination centre to support)
• Code repository/wiki for implementation snippets

Dissemination

Session at next Insight Net meeting:

1. Introduction to challenges (talk)
2. Challenges discussion with group
3. Introduction to modelling opportunities (talk)
4. Modelling opportunities discussion
5. Decision tree and method selection (presentation + discussion)

Repository structure

• manuscript/ - Content plan and drafts
• user-submitted-snippets/ - Code snippets and notebooks from users (future)
• guidance-website/ - Guidance website content (future)
• meeting/ - Meeting planning and feedback
• resources/ - Reference materials and archived plans

Running the analysis

Prerequisites

1. Quarto: Follow the instructions at quarto.org to install Quarto.

2. Task (optional): Install Task for automated workflow management.

Using Task (recommended)

task

Available tasks:

• task - Render all documents (default)
• task render-paper - Render the manuscript
• task preview - Preview manuscript with live reload
• task install-extensions - Install Quarto extensions
• task --list - Show all available tasks

Manual execution

1. Install Quarto extensions:

   quarto add kapsner/authors-block --no-prompt

2. Render the manuscript:

   quarto render manuscript/paper.qmd

Citation

Citation information will be added upon publication.