Setup Guide

Modified

May 11, 2026

Do this the day before the workshop. If anything goes wrong, fixes are easier in your own time than in a packed conference room with patchy wifi.

1. Install R

Download R (version 4.1 or later — we use the native |> pipe). Default installer options are fine on every platform.

2. Install RStudio Desktop

Download RStudio Desktop (free version). Open it once after installing to confirm it launches.

3. Clone (or download) this repository

git clone https://github.com/drarunmitra/idm-jhapsmcon-2026.git
cd idm-jhapsmcon-2026

Use the green Code → Download ZIP button on the repo page, then unzip.

4. Open the R project

Double-click IDM_EFICON2024.Rproj (or use File → Open Project… in RStudio). This sets the working directory and ensures the here() package finds files correctly.

5. Install the workshop packages

In the R console:

source("setup.R")

This runs a one-time package install via pak. Plan for 5–15 minutes depending on your network and how many packages you already have. The script will:

Install pak if missing
Configure the Epiverse-TRACE R-Universe repository
Install everything you’ll need across all five sessions

If a package fails to compile, install Xcode Command-Line Tools (macOS) or Rtools (Windows) and retry.

6. Verify the COVID-19 India dataset

file.exists(here::here("data", "covid_india_daily.csv"))
#> [1] TRUE

If the file is missing (e.g. you pulled a fresh checkout and want the latest data):

source(here::here("data", "prepare_covid_india_daily.R"))

This rebuilds the dataset from the JHU CSSE upstream — see the Data page for details.

7. Quick sanity check

Paste this into the console — it should return a tibble with three waves’ worth of daily case counts.

library(tidyverse)
library(here)

read_csv(here("data", "covid_india_daily.csv"), show_col_types = FALSE) |>
  arrange(desc(daily_confirmed)) |>
  head()

If you see the May 2021 peak day at the top of the output, you’re ready.

Optional but recommended

GitHub account — fork the repo, push your activity scripts, share with peers.
The codefrag Quarto extension — if you’ll rerender the decks yourself: quarto add mcanouil/quarto-revealjs-codefrag from inside the project root.

Need help?

Open an issue on GitHub or reach out before the workshop. Setup issues are much harder to fix in the room.