Lab Sessions: R Tools for Rapid Outbreak Analytics

SISMID 2026 · Lab Sessions

R Tools for Rapid Outbreak Analytics

Synchronous lab sessions — June 25–26, 2026

Below you will find materials, readings, and files for each of your four lab sessions. Lab files are available on the course GitHub repository.

← Back to module page

About the lab sessions

Lab 1

Outbreak Early Phase

Critical data husbandry and management techniques and early phase analyses that are critical to resolving uncertainty.

Lab 2

Outbreak Middle Phase

Real-time analysis tools critical to situational awareness and advanced analyses for parameter estimation.

Lab 3

Outbreak Reconstruction — Part 1

Introduction to outbreak reconstruction using the outbreaker2 R package. Students will learn the conceptual foundations and applied techniques for reconstructing transmission chains using epidemiological, genetic, and contact data.

Lab 4

Outbreak Reconstruction — Part 2

Assess model performance and extract key insights from outbreak reconstruction using the RECON ecosystem.

Lab sessions

Lab 1
Day 1

Thursday, June 25, 2026
1:00 – 2:30 PM ET

Outbreak Early Phase

This session introduces critical data husbandry and management techniques and early phase analyses that are critical to resolving uncertainty. Review the related materials, work through the lab workbook, and then participate in the interactive session where we will complete some guided exercises.

Video
Pre-session video

Please review the Early Phase video on the pre-session materials page before attending this lab.

Lab file
lab_1.qmd

Available in the GitHub repository. Use assorted tools to review early outbreak data, prepare visualizations, and make critical initial parameter estimates.

Readings

Early Outbreak tutorial — Epiverse
Ebola Case Study Part 1 — Recon

▶

Session recording

Recording will be posted here after the session.

Lab 2
Day 1

Thursday, June 25, 2026
3:00 – 4:30 PM ET

Outbreak Middle Phase

This session introduces real-time analysis tools that are critical to situational awareness and advanced analyses for parameter estimation. Review the related materials, work through the lab workbook, and then participate in the interactive session where we will complete some guided exercises.

Video
Pre-session video

Please review the Middle Phase video on the pre-session materials page before attending this lab.

Lab file
lab_2.qmd

Available in the GitHub repository. Use assorted tools to prepare short-term forecasts and estimate various epidemiological parameters from data.

Readings

Middle Outbreak tutorial — Epiverse
Ebola Case Study Part 2 — Recon

▶

Session recording

Recording will be posted here after the session.

Lab 3
Day 2

Friday, June 26, 2026
1:00 – 2:30 PM ET

Practical 1: Outbreak Reconstruction — Part 1

This two-part lab introduces outbreak reconstruction using the outbreaker2 R package. The course combines pre-recorded videos, readings, and hands-on practicals. Students will learn both the conceptual foundations and applied techniques for reconstructing transmission chains using epidemiological, genetic, and contact data using R and the RECON ecosystem.

Lab file
lab_3.qmd

Available in the GitHub repository. Use outbreaker2 to reconstruct outbreaks using epidemiological, genetic, and contact data.

In this lab you will

Load and prepare epidemiological, genetic, and contact data
Fit the outbreaker2 model
Review an overview of the default results

▶

Session recording

Recording will be posted here after the session.

Lab 4
Day 2

Friday, June 26, 2026
3:00 – 4:30 PM ET

Practical 2: Outbreak Reconstruction — Part 2

Lab file
lab_4.qmd

Available in the GitHub repository. Learn how to assess model performance and extract key insights from outbreak reconstruction.

In this lab you will

Assess model convergence using coda and mixtree
Summarise and interpret output using o2ools (accuracy, entropy, reproduction number)
Estimate transmission patterns with linktree

▶

Session recording

Recording will be posted here after the session.