Welcome

This collection was inspired by Chrissy Roberts’ Code Book, which I was introduced to by Caitlin Bourke. It brings together the most useful pieces of code I’ve accumulated over the years—scripts I often return to or have developed for specific analyses. My hope is that future me (and anyone else who happens to come across this) finds it a helpful and practical resource.

Here are a list of my favourite R packages that will be leveraged throughout this section.

Data Wrangling

library(tidyverse)
library(janitor)

Epidemiology / Statistical Analysis

library(tidyverse)
library(janitor)
library(gtsummary)

Population Genetics Analysis

library(poppr)
library(adegenet)

R Shiny

library(shiny)
library(shiny.fluent)
library(waiter)

R Package Development

library(devtools)
library(usethis)

General Git things

Making changes

git add .
git commit -m "Add a personalised and detailed message"
git push

Clone a repository from GitHub

git clone <<INSERT GITHUB REPOSITORY>>

How to remove a repository on Github

1. Go to the repository’s main page on GitHub (e.g., https://github.com/yourusername/pvsero)
2. Click Settings (right-hand tab)
3. Scroll all the way to the Danger Zone at the bottom
4. Click Delete this repository
5. GitHub will ask you to:
   • Confirm the name of the repo (e.g., yourusername/pvsero)
   • Type it in to confirm
6. Click the red I understand the consequences, delete this repository button

The repository will be permanently deleted — this action cannot be undone.

This does not delete your local R project or files — only the copy on GitHub. If you want to disconnect GitHub but keep the local Git repo, you can just remove the remote link using: git remote remove origin