R object-oriented programming and package development

Prerequisites

The course will teach intermediate R object-oriented programming and how to build a fully functional R package.

The course page includes slides and handouts; other relevant teaching materials are available here) and the sequences example package used as template in the course can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
• Further details regarding eligibility criteria are available here

• A good knowledge of R and some active programming experience is required.
• Only attending Introduction to R would not provide sufficient background for this course.
• Familiarity with object-oriented programming would be an advantage, but is not essential.

Number of sessions: 1

Bioinformatics, Software engineering

After this course you should be able to:

• use object-oriented programming in R and build your own packages

During this course you will learn about:

• What is object-oriented programming; description of the working example; R programming best practices: tips and tricks, environments, coding standards
• R object-oriented programming: the S3 and S4 OO systems
• Documentation: documenting functions, methods and data, providing executable examples; documentation using Roxygen; executing R
• Writing R packages: minimum package structure; combining the written classes/generics/methods and documentation to create a package; building, checking and installing packages
• Other advanced R programming topics: testing code, unit testing; profiling and debugging; calling C code inside R

Presentation and demonstrations

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1 day

A number of times per year

• An Introduction to Solving Biological Problems with R