Additional resources for getting further with R

1. Downloading R and RStudio on your own computer

R and RStudio are free to download and use. Go to https://posit.co/download/rstudio-desktop/. Note that you have to download both R and RStudio. If you are using a university or research institute computer, your institution’s software distribution system probably has R and RStudio available.

Next, install some packages. A good start would be tidyverse that we used on the course, which is actually a collection of many useful packages. The easiest way is to use the the Packages tab -> Install in the lower right panel of RStudio. You can also use the command line:

install.packages("packagename")

Most packages come from CRAN, R’s central software repository. Other common sources are Bioconductor and Github. Note that they require different installation commands. When in doubt how to install a package, check the package manual or website.

2. Websites and books

There are lots of great books, websites and online tutorials for learning more about R. Some examples:

• R for Data Science (free e-book) A great tidyverse-based resource.

• Modern Statistics with R (website and book) An up-to-date introduction to R and data wrangling that goes deep and wide into statistical analyses with R.

• Programming with R (website) A more programming-oriented R introduction from Software Carpentry that covers for example creating functions and best practices for writing R code.

• Deep R Programming (website and pdf) A more advanced programming-oriented introduction to R.

• Getting Started with R: An Introduction for Biologists (book)

• Riffomonas Code Club Youtube channel and R scripts. R basics and more advanced tricks especially for microbial ecologists.

• Cookbook for R (website) Check for example the section on graphs (lots of information on fine tuning your ggplot2 plots).

• Big Book of R (website) A huge collection of R resources.

• Applied Statistics with R (free e-book)

• Learning Statistics with R (free e-book)

• An Introduction to R (free e-book) Covers also the basics of R Markdown and version control.

• swirl: an R package for interactive self-learning within R

3. Resources for working with and choosing colours in R

• Working with colours in R
• Colour scales and legends
• Paul Tol’s colur schemes
• ColorBrewer and the R package RColorBrewer

4. R cheat sheets

Cheat sheets are handy collections of commands and options on a specific package or a topic. Here are some examples:

• ggplot2 for plotting
  
• data manipulation with dplyr
  
• data tidying with tidyr

5. Using R on CSC’s supercomputers

If get to the point that your R scripts are too computationally heavy to run on your own computer, it might be time to look for extra resources. R is available on CSC’s supercomputer Puhti. Like many CSC’s services, Puhti is free to use if you are affiliated with a Finnish higher education institution or a state research institute. An introduction to using R in CSC’s services is available as slides here and as a talk here, and further instructions on using the Puhti R environment can be found in R documentation.