Infectious Disease Modelling in R

JHAPSMCON 2026 · 4ᵗʰ Annual Jharkhand State Conference of IAPSM

Published

May 9, 2026

A one-day, beginner-friendly workshop. By 5 pm you will be able to read every line of code behind a working Rt analysis — and recognise every panel in a real public-health dashboard.

Quick start

TipNew here?
  1. Open the Setup guide and install R, RStudio, and the workshop packages (source("setup.R")).
  2. Skim the Schedule below.
  3. The night before the workshop, run the data prep script so the COVID-19 India dataset is ready locally.

Schedule

Time Session
10:00–11:00 1. Foundations — Why model · R0 / Rt
11:00–11:15 ☕ Tea
11:15–12:15 2. Just Enough R — basics · tidyverse · ggplot · applied Rt
12:15–13:15 3. Compartmental Models — SIR / SEIR + extensions
13:15–14:15 🥗 Lunch
14:15–15:15 4. Scenario Modelling — counterfactual + 3 interventions
15:15–15:30 ☕ Tea
15:30–16:30 5. AMCHSS COVID-19 Dashboard — guided walkthrough
16:30–17:00 Q&A and Wrap-up

Sessions

1 · Foundations

Why model? R0 ranking. Rt in one line. Forward vs. inverse problems.

2 · Just Enough R

R basics, tidyverse, ggplot2, then estimate Rt from real Indian COVID-19 data.

3 · Compartmental Models

SIR with deSolve, SEIR, extensions (SEIRS, SEIRD), four-disease group work.

4 · Scenario Modelling

A COVID-like scenario with three interventions (NPI, vaccination, combined) vs. counterfactual, using epidemics.

5 · AMCHSS Dashboard

Guided walkthrough of the AMCHSS COVID-19 dashboard — every panel mapped to a concept from the day.

What you’ll take home

  • A working R + RStudio setup for infectious disease modelling.
  • Six rendered slide decks, downloadable.
  • A library of hands-on R scripts you can adapt to your own data.
  • The COVID-19 India daily-case dataset (JHU CSSE), pre-cleaned for analysis.
  • A printed cheat-sheet covering tidyverse verbs, the line-list pipeline, and the “which tool when?” decision aid.

Team

Dr. Arun Mitra Peddireddy · Prof. Biju Soman · Dr. Adrija Roy. See the About page for full credits and attribution.

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