L0 setup

Self-study. Not graded. Takes about 30 minutes, most of it waiting for downloads.

The first session covers the course, the project, and your R + GitHub setup. You will get much more out of it if the software is already installed. Everything afterwards assumes it works.

If something fails, stop and bring it to the first session — that is what it is for. Do not spend two hours fighting an install alone.

The checklist

1. Install R

https://cran.r-project.org/ — choose your operating system and take the latest release. The course is developed on R 4.5.1; anything from 4.3 upward is fine.

Install R before RStudio. RStudio is an editor; it needs R underneath and will not find it if the order is reversed.

2. Install RStudio

3. Install the PDF toolchain

This is the step that most often goes wrong, and the one worth doing beforehand rather than during a lab. In the RStudio console:

install.packages("tinytex")
tinytex::install_tinytex()

The second line downloads a small LaTeX distribution and takes a few minutes. You do not need MiKTeX or MacTeX; TinyTeX is enough and much smaller.

4. Install the course packages

install.packages(c(
  "rmarkdown", "knitr", "tidyverse", "haven",
  "survival", "survminer", "rms", "survey",
  "mice", "tableone", "nhanesA", "kableExtra"
))

Two more are needed later — Publish from Lab 3, interactionR from Lab 4 — and you can install them now:

install.packages(c("interactionR", "Publish"))   # note the capital P

If a package fails to install, note which one and the error message. Bring both.

5. Create a GitHub account

https://github.com/signup — free. You will keep your group’s code in a repository and submit a downloaded zip of it with M1 and M4 — the only two milestones that ask for one. We do not need access to your repository, so a free personal account is all you need.

6. Test that it works

Create a new file in RStudio (File → New File → R Markdown), replace everything in it with the text below, save it as setup_test.Rmd, and click Knit.

---
title: "Setup test"
author: "Your name"
output: pdf_document
---

```{r}
sessionInfo()
```

```{r}
library(ggplot2)
ggplot(mtcars, aes(wt, mpg)) +
  geom_point() +
  labs(title = "If you can see this plot in a PDF, your setup works")
```

You are done when a PDF appears containing your session information and a scatter plot.

If PDF fails but HTML works, the problem is step 3 — TinyTeX. That is a common and fixable problem; bring it to the first session.

What to bring to the first session

Once the in-person labs begin, you will need your laptop with R installed at every one. The syllabus gives the lab day, time and room.

If you don’t have a suitable laptop

Contact the instructor. UBC Library lends laptops, and the UBC Vancouver Technology Bursary may be able to help. Required software for this course costs $0 — R, RStudio, TinyTeX, GitHub and both textbooks are all free.

L0: Setup — do this before the first class