During this course we will use the following software and services:
You will need to install the software and register for these services on your own. While we will use one session for joint troubleshooting, it is absolutely necessary that you do your best to install the software on your own before that date. To this end, this document is meant to provide you with all the information needed. If you have questions, please use the Moodle forum. It is very unlikely that you are the only person having a particular problem. Maybe others can already help you out, and if not, all should benefit from the solution we find for your problem together.
Please also note that there is a separate tutorial on how to install the packages (a.k.a. R extensions) that we are going to use over the semester. Its best to continue with this tutorial on installing the required R packages directly after you have complete this one.
R is the programming
language we are using. Installing R basically gives your
computer the ability to understand commands you will issue to it using
the language R. R-Studio is an application that
facilitates the development of R code. It is a so called
Integrated Development Environment (IDE). You may think of it
as a fancy editor, which not only allows you to write programs in
R using a more elaborated text editor, but simultaneously
lets you preview the graphs you are designing, or the reports you are
writing. Because R-Studio facilitates the use of R, it is
important to install R first, and then install R-Studio
second.
Git is a so called version
control system (VCS). It allows you to keep track of different
versions of your scripts without saving them under different names. In
other words, if you use Git, you can dispense of saving
Script-v1.R, Script-v2.R and
Script-v3.R, but instead only keep Script.R
and save the different versions in the background, together with some
comments about what you have changed. Moreover, it facilitates the joint
work on the same document, something that is tremendously helpful for
group works. While we will not learn how to use Git (I will provide some
optional tutorials, though), it is important to install it since many
user-written features of R are distributed in a way that relies on
Git.
Github can be thought of as a
server for Git. R is an open source programming language
with a very active community. Many people are constantly developing new
features for R. For instance, if a new prediction algorithm
get developed, some people will soon write a so called R-package that implements this algorithm
in R. Then you as an R user can download this package and
use the new algorithm. This way, R is unlikely to ever
become outdated. Since most developers use Git when developing the
packages, they often distribute the programs in a way that aligns well
with the use of Git. And the most prominent way is Github.
Thus, you can view the source code for almost all R
packages you will be using via Github. Github is free, and all you need
is to register!
The final service we will be using is Netlify. It is an easy way to publish reports and host small websites. We will use it such that you can create reproducible reports and present them in a visually appealing way. Given the ease of use, it is a great tool if you want to polish your results up visually and send them to friends or colleagues who might not even use R themselves.
The information in this tutorial is provided for Mac OS, Windows, and Linux. Given the variety of different Linux distributions the comments on the latter are rather short. There are, however, plenty explanations to be found on the web for many different Linux distributions.
After you have completed the steps outlined below you are almost done: all what remains is to install the R packages we require over the course of the seminar. To this end, please consult the respective Tutorial.
The installation of R is very similar across operating
systems (OS). The easiest way is to visit the R Homepage and to download the
most recent version for your OS. In case you are using Mac OS and want
to use Homebrew, its best to use this formula.
Important for Mac user: There are different versions
of R for Intel chips, and Apple chips (M1, M2, etc.). It is
very important that you install the correct version. If you are not sure
whether your Mac contains a chip from Intel or Apple, click on the Apple
symbol in the upper left of the screen, then click on
About this Mac and you can see which processor your Mac is
using in the new window. If you have an Apple chip, always install R for
the so called arm64 architecture. Intel chip users must use
the x86_64 architecture instead.
If you are using Windows, it is necessary to install
RTools, which is required if you want to use packages
written by others that are not officially released. To do so, simply
visit the
following website, download the installer, and install the
software:
When asked during the installation process, do not select
the box for Add rtools to system PATH, but do
select the box for
Save version information to registry.
The Command Line Developer Tools could be thought of as the Mac pendant to RTools. These allow you to build R packages from source (meaning, basically, you can use packages that are in early stages of distribution, or packages that are not released on the official R servers).
The easiest way to install them is to open the App
Terminal, and then to type
xcode-select --installand press Enter. Then a pop up window will open and
allow you to install the software.
In case R is already installed on your computer you should make sure
that your version is more of less up to date. For our seminar you should
use at least R version R 4.1.2. The version you are
currently using is shown as soon as you start R.
Please note: if you installed R anew in the previous step, you do not need to update it. The information on updating R is mainly relevant for people who have installed R already some time ago.
For MacOS users, the easiest route to update
R is to just re-install the most current version from the
R Homepage. Keep in mind that
in this case you might need to re-install all previously installed
packages. If you have a lot of packages installed that you want to keep,
the following steps facilitates the re-installation process. First, save
a list with all the packages you installed yourself. To this end type
the following into the R console:1
package_overview <- installed.packages()
package_names <- as.vector(
package_overview[is.na(package_overview[,"Priority"]), 1])
save(package_names, file="r_packages.rda")After re-installing R, you then need to load the file you previously
saved and identify the missing packages. You can use the following code
to do so if you are in the working directory in which you saved the file
"r_packages.rda":
load("r_packages.rda")
packages_new <- installed.packages()
packages_new_ <- as.vector(packages_new[is.na(packages_new[,"Priority"]), 1])
missing_packages <- setdiff(package_names, packages_new_)
install.packages(missing_packages)
update.packages()Windows users have a slightly more convenient route available to them: the installr package. It does not require you to re-install your packages. Just type the following code into your R console:2
install.packages("installr")
ibrary(installr)
updateR(TRUE)For more information see the package website.
Linux users simply install R via their package manager.
A quick search on Google should provide you with the information that
are relevant for your particular Linux distribution. Updating is usually
straightforward as well: just run the respective command from your
package manager.
Installing R-Studio is easy. The only thing you should keep in mind
that you should install R first, and R-Studio
second. So, after installing R got to the R-Studio
download page and download the RStudio Desktop version for
your OS according to the installation instructions provided.
If you are on Mac and you are using Homebrew you may use this formula.
If you want to update R-Studio, you just install it again. Please
note that the minimal version for this seminar should
be RStudio 2022.07.1+554.
Installing Git is straightforward, but the right approach depends on your OS.
On MacOS you should install Git as part of the Command Line Developer Tools, which themselves are part of XCode (see above). Its easiest to run the following command from your Terminal:3
git --versionIf you get an output such as git version 2.34.1 you
already installed you need. If not, you will be asked to install the
respective software packages (see above).
On Windows you download Git for Windows
from the official
Webpage, which also provides you with all the relevant
instructions.
On Linux use you package manager. In most cases the
name of the relevant package is git-all, so on Ubuntu, for
instance, you would install Git via
sudo apt install git-all.
This is easy. Just visit https://github.com/ and sign up using your email account.
This is easy as well. Visit https://www.netlify.com/ and click
on Sign up in the upper right of the webpage. You can now
either create a Netlify account by clicking on Email and
register a new email address, or you can link Netlify to one of the
other accounts you might already have. I personally, for instance,
linked Netlify to my Github account.
Once you finished with installing all the relevant software described
in this post I recommend you continue directly with the second (and
last) installation tutorial
that assists you in installing the R packages required over
the course of the semester.
And, by the way, if this installation process seems frustrating to you: don’t worry, its the only time during the semester you need to install anything;)
If you do not yet know what the R console is don’t worry. You will learn this during the course. But for now it would then be better to update R by just re-installing it.↩︎
If you do not yet know what the R console is don’t worry. You will learn this during the course. But for now it would then be better to update R by just re-installing it.↩︎
By this I mean that you first open the app
Terminal and then enter the commend into the window that
has opened, and then press Enter.↩︎