Check your setup

Packages and verification

Install the workshop packages

Open your meded-conclave-2026 project in RStudio. Paste this into the Console and press Enter. It will take 10–20 minutes on a first run. Start it and make tea.

pkgs <- c(
  
  # Core
  "tidyverse",     # dplyr, ggplot2, tidyr, readr, stringr, forcats
  "here",          # sane file paths
  "janitor",       # clean_names(), tabyl()
  
  # Tables
  "gtsummary",     # publication-ready tables
  "gt",            # the table engine underneath
  "flextable",     # tables for Word output
  
  # Reporting
  "quarto",        # render .qmd from R
  "knitr",
  "rmarkdown",
  "rstudioapi",    # lets the setup check read your RStudio version

  # Data and extras
  "skimr",         # fast data overviews
  "scales",        # axis formatting
  "patchwork",     # combine ggplots
  "MASS"           # classic datasets from Venables & Ripley
)

install.packages(setdiff(pkgs, rownames(installed.packages())))
WarningOne thing to know about MASS

MASS has its own select(), so loading it after dplyr silently replaces the dplyr one and select(students, batch) starts failing with a confusing error. Load MASS first, or leave it unloaded and reach for a dataset with MASS::Boston. If select() ever stops behaving, run conflicts().

WarningIf you are asked “Do you want to install from sources…?”

Answer No (type n, press Enter). Binary packages install in seconds; source packages compile for minutes and sometimes fail. You do not need the newest possible version for this workshop.

Run the verification script

Download check_setup.R, put it in your project’s R/ folder, then run:

source("R/check_setup.R")

The script checks eight things: your R version, the native pipe, RStudio, Quarto, all sixteen required packages, whether the core stack loads, whether your project folder is writable, and whether Quarto and R can complete an end-to-end render together.

What a healthy result looks like

── MedEd Conclave 2026 · setup check ───────────────────────────
✔ R version 4.6.1 (2026-06-24) (need >= 4.1.0)
✔ Native pipe |> works
✔ RStudio 2026.08.0
✔ Quarto 1.10.18
✔ All 16 required packages installed
✔ Core packages load cleanly
✔ Project directory writable (meded-conclave-2026)
✔ Test render (HTML) succeeded
────────────────────────────────────────────────────────────────
You are ready for 9 September. See you there.

Any line starting with ✖ needs attention before the workshop. Send the whole output to the SET Team if you cannot resolve it. The individual lines tell us exactly what is wrong, which turns five emails into one.

Test that Quarto renders

The single best proof that everything works end to end:

  1. File → New File → Quarto Document
  2. Title it test, choose HTML, click Create
  3. Click Render (or Ctrl/Cmd + Shift + K)

A browser tab should open with a formatted document containing a plot. If it does, your entire toolchain works and nothing on Day 1 can be blocked by installation.

TipSave the evidence

Take a screenshot of a successful render and bring it. If something breaks on the day, knowing it worked last week narrows the problem down enormously.

Common results and what they mean

Line Means Do this
✖ R version ... too old R below 4.1, so the native pipe will not work Install R 4.6.x from CRAN
✖ Quarto not found Quarto is not on your PATH Reinstall Quarto, restart the computer, then install.packages("quarto")
✖ Quarto X is installed, but the quarto R package is not Quarto itself is fine; R just cannot talk to it install.packages("quarto")
✖ N package(s) missing An install silently failed Re-run the install line the script prints
✖ Cannot write to ... Project is in a restricted or cloud-synced folder Move it to Desktop or Documents
✖ Test render failed R and Quarto are both present but not co-operating See Troubleshooting
! Cannot read the RStudio version The rstudioapi package is missing install.packages("rstudioapi")
! Not running inside RStudio Not an error Ignore it if you use another editor

Send us your result

Do this even if every line passed. It is how we know who is ready and who needs help before 9 September.

  1. Select the whole setup-check output in the Console and copy it, or take a screenshot of it.
  2. Go to the Moodle course, open Get your laptop ready → Show us your setup check passed.
  3. Paste the output in the text box, or attach the screenshot. Then submit.

Something failed and you cannot fix it? Submit it anyway, exactly as it is, and add one line saying which operating system you are on. A failed check we can see on 25 August is a five-minute fix. The same failure discovered at 09:15 on 9 September costs you the first session.

Next

→ R primer: The Basics of R so that you are ready for Day 1!!

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