Programming in R

Course manual 2023/2024

Course content

The ability to create, understand and scrutinize computer code is an extremely important skill set throughout academia, but especially so in interdisciplinary work. Computer code and, more generally, computational thinking, forces us to follow standards, be precise in definitions and be explicit about what we assume and what we mean exactly by our concepts or models. Computational thinking enhances our ability to exchange and link ideas, knowledge and data across disciplines.

This course is aimed at : 1) teaching basic coding skills (and some general computational skills) to get concrete scientific data and modelling tasks done, and 2) enhancing creative and critical thinking skills.

The coding skills concern data processing, visualization and the implementation of (mathematical and conceptual) models in computer code. Creative and critical thinking focuses on the translation from algorithm to code, comparison of different implementations, debugging and code documentation.

In this course, we will work with the R programming language and use the RStudio development environment (if needed, you find download and installation instructions for Windows and macOS on Canvas). The textbook An Introduction to Data Analysis in R will be used as the main study text. A digital version of book is available for you for free in the UvA library if you are logged in to the eduroam network at Science Park (you can download a pdf or epub copy for off-line use).

Study materials

Practical training material

• manual at https://uva.sowiso.nl

Software

• R and RStudio (freely available - see installation instructions for Windows and macOS on Canvas)

Other

• the textbook An Introduction to Data Analysis in R (freely available online and as pdf-download when logging in via the UvA eduroam network or VPN)

Objectives

• operate an integrated development environment (RStudio) to enter/edit code, run code and view output
• document own code
• troubleshoot programming problems ("bugs") systematically
• know and implement basic R syntax for basic mathematical calculations and data handling (type conversion, selecting, merging, aggregating, sorting)
• create appropriate figures to visualize data in R
• implement control structures for conditional branching (if-else) and iteration (for- and while-loops) in R
• import/export and parse basic data formats in R
• illustrate with an example how code enables scientific data analysis

Teaching methods

• Self-study
• Lecture
• Computer lab session/practical training

There are weekly lectures where overarching concepts are explained and an overview of the material for the coming week is provided. To acquire R coding skills and get sufficient practise, students will complete the exercises at  https://sowiso.uva.nl by self study and during computer practicals (two per week). During practicals, students get additional explanation on the material and can ask questions. Attendance to the practical is compulsory.

Learning activities

Attendance

Programme's requirements concerning attendance (OER-B):

• Participation in fieldwork is compulsory and cannot be replaced by assignments or other courses.
• In case of practical sessions, the student is obliged to attend at least of 90% of the sessions and to prepare himself adequately, unless indicated otherwise in the course manual. In case the student attends less than 90%, the practical sessions should be redone entirely.
• In case of tutorials/seminars with assignments, the student is obliged to attend at least 7 out of 8 seminars and to prepare thoroughly for these meetings, unless indicated otherwise in the course manual. If the course has more than 8 seminars, the student can miss up to 1 extra meeting for every (part of) 8 tutorials/seminars. If the students attends less than the mandatory tutorials/seminars, the course cannot be completed.

Additional requirements for this course:

For students who follow this course for the first time, the computer practicals are compulsory. A maximum of 1 from the 7 practicals can be missed. For students who have to retake this course, attendance is not compulsory.

In general, attending all scheduled education activities is strongly advised. By doing so, you actively contribute to a lively learning community and significantly improve your chances of successfully completing the course. The designated mandatory activities play a crucial role in achieving the course objectives and are essential for your overall progress. By registering for this course, you are complying with the rules regarding attendance and agreeing to actively prepare for and participate in the mandatory activities.

Assessment

This course assessed by a single graded exam at the end of the course, which makes up 100% of the assessment. The exam will contain the same kind of programming problems as those studied during the course.

Assessment diagram

Students that were enrolled in the course in previous years

Students who were enrolled in the course in previous years are advised to attend all computer practicals, but attendance is not mandatory for them.

Assignments

Students have to send-in homework assignments on canvas before every practical (pass/fail). If all 7 homework assignments are not made, the student cannot take the exam.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Honours information

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Additional information

It is important that everyone feels safe at the UvA and Future Planet Studies. We are committed to provide social safety and we offer various forms of support for people experiencing inappropriate or unsafe situations. Consult the UvA website or Future Planet Studies Canvas page for more information and contact info.

Last year's student feedback

Compared to the material from last year, completely new material has been selected for the course content, and a new set of matching exercises have been created.
Also, a starting lecture and short overview-lectures to provide introductions at the start of each practical have been created.

Contact information

Coordinator

• dr. ir. E.E. van Loon

Staff

• Emiel van Loon
• Walter van Dijk
• Phil  Grammel