Chapter 4 Beyond the Basics

4.1 Git & R

We will not get into the details of git. But - RStudio has a git plugin and the book Happy git with R will git you all set.

Source Happy Git with R by Jenny Bryan

Alternatively, you can use gist.github.com to share & store code snippets, notes, thoughts and blog posts.

4.2 Examples of R in the wild

Here are some examples of R.

• Research compendium:
  • Estimating the effect of the 2005 change in BCG policy in England: A retrospective cohort study by Sam Abbott.
  • Repurposing antihypertensive drugs for the prevention of Alzheimer’s disease: a Mendelian Randomization study by Venexia M Walker.
  • Fat distribution GWAS by Sara Pulit.

• Data Journalism: Roger Federer: 20 years, 20 titles by SRF Data.

• Blogpost: The evolution of a ggplot by Cederic Scherer.

• Animations by Garrick Aden-Buie.

• Fun stuff like creating memes by Danielle Navarro.

• Blogpost on replication: Analysing the mouse microbiome autism data by Thomas Lumley.

• API blogpost by Heather Nolis and Jacqueline Nolis.

• Web application with Shiny: iSEE by Kevin Rue, Charlotte Soneson, Federico Marini and Aaron Lun (Winner of the Shiny Contest 2019).

4.3 Neat packages & functions

Data import

• data.table: (Fast) alternative to readr.
• datapasta: Copy + paste unconventional tables.
• fabricatr: Imagine your data before you collect it
• Practical recommendations for organizing spreadsheet data in a way that both humans and computer programs can read: Data Organization in Spreadsheets by Broman & Woo (2018).

Data exploration

Summarising data with:

• vtable
• skimr
• DataExplorer

Data manipulation

• data.table: (Fast) alternative to dplyr.
• janitor: data cleaning.

Data visualisation

• esquisse to interactively create a plot.
• many other #dataviz libraries in R: gganimate, plotly, vegalite
• Publication ready plots with cowplot and ggpubr
• Pick a chart type with R Graph Gallery

ggpubr

holepunch

Make your package binder-ready with holepunch.

Source: github/holepunch

Best practices

• Adhering to style guides with styler.
• Unit tests and sanity checks with testthat and assertr.
• Write functions and package them with devtools and usethis.
• Makefile-like workflows with drake.