During this course we will use the following software and services:
There is a separate tutorial on how to install the packages (a.k.a. R extenstions) that we are going to use over the semester. You go continue with this tutorial directly after you have complete this one.
You will need to install the software and register for these services on your own. While we will use one session in the second week 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.
R is the programming
language we are using. Installing R basically gives your
computer the ability to understand commands you will give to it using
the language R. R-Studio is an
application that facilitates the development of R-Studio. 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.
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. Sine 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 see the source code for almost all R packages you will be using on 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 the 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 too 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.
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 4.0.4. 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.
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 Ubunto, 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.
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.↩︎