Install R

is available for free for Windows, GNU/Linux and macOS.
As for now, the latest version is 4.1.1.

One common complain about R is the frequency of updates. This is true, but can be sorted out with a good package manager. Of note, major updates are the only one forcing you to re-install extra-packages and are released on a yearly basis.

Windows

Visit the download page and choose the corresponding installer for your platform. Mind that you will need Rtools of the same version as your to compile and install some packages.

macOS

You browse to the download page and take it from there.

GNU/Linux

Any GNU/Linux distributions is bundled with a great package manager such as dpkg or rpm. Visit the appropriate web-page for your distribution here.

After you get the correct entry in your package manager, it should be quite easy as:

sudo apt-get install r-base r-base-dev

Install RStudio

RStudio is an Integrated Development Editor, it wraps and interfaces and needs to be installed first. The free-version contains everything you need.

Visit the download page and choose the corresponding installer for your platform. As for now, the latest version is 1.4.1717.

Check the release notes to see if an update would be useful.

Open RStudio

They are 4 main panels in RStudio, but as the top-left is for scripting and by default missing, the layout should looks like

Of note, the default theme is with a white background. You can change it in the Global options > Appearance > Editor theme. Here is displayed the Cobalt theme.

Install R packages from the Comprehensive R Archive Network (CRAN)

On the bottom-right panel, 5 tabs are present:

  • Files
  • Plots
  • Packages
  • Help
  • Viewer

Click on the Packages tab (1.) and select the select the Install button (2.). Type dplyr in (3.). You will see the word auto-completion that helps.

It takes some time, usually 10 seconds up to several minutes for a single package depending on its size and compilation stage.

The packages can also be installed in the console (i.e. the bottom-left panel). The snapshot below shows you how to install remotes using the console:

Of note, remotes is handy when you want to install a development version, for example for a new feature or if a bug was fixed but the package not yet on CRAN.

remotes::install_github("r-lib/remotes")

A note about package updates

The complaint of very frequent updates might be legitimate as it could be cumbersome to maintain R up-to-date when you have many packages. Actually, it is as easy as:

update.packages()

But, you could also use the green Update button next to the Install (located in the Packages tab). The advantage is that you can check which package you would like to update and look at the actual changes by clicking on the NEWS link.

Installing the tidyverse

Installing the tidyverse is straight-forward using the package manager in RStudio. You can also use the command line.

install.packages("tidyverse")

If you have several cores, you may speedup the install with multi-threading (here for 2 cores):

install.packages("tidyverse", Ncpus = 2L)

Dependent libraries

Several libraries are mandatory for successfully installing the tidyverse. If you encountered issues, install them with:

GNU/Linux

in a terminal, :

sudo apt install -y libcurl4-openssl-dev libssl-dev libxml2-dev

Then install the tidyverse as above.

Testing your installation

Copy / paste the code below and you should obtain the following plot.

It ensures that you are using R version >= 4.1 and readr >= 2.0.

library(tidyverse)
read_csv("https://biostat2.uni.lu/practicals/data/swiss.csv",
         show_col_types = FALSE) |>
  pivot_longer(cols = c(Fertility, Agriculture),
               names_to = "measurement", 
               values_to = "value") %>%
  ggplot(aes(x = value, y = Education, colour = measurement)) +
  geom_point() +
  geom_smooth(method = "loess", formula = "y ~ x") +
  theme_bw(14)

If not, please contact Aurélien Ginolhac with the error produced.

Installing Bioconductor

The Bioconductor resource is an indispensable collection of packages for the interpretation of biological data. It is not an essential part of the workshop but some practicals make use of it. To save time, copy / paste the following code into the console to install for example the GEOquery package:

# to install the version 3.12 of the bioconductor installer.
install.packages("BiocManager")
BiocManager::install("GEOquery")

You might be asked if you want to update some / all / none packages.

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