Open Science, R, & RMarkdown

You were introduced to Open Science practices, RMarkdown, and RStudio when you completed a protocol and subsequent Recommendation Report in BIOL 125. We will be using a similar format and template for your 3rd and 4th assignments in BIOL 205.

Protocols are frequently not formally peer-reviewed. However, there is a specific publication type known as a Registered Report, in which peer-review of a protocol is an integral part. In a Registered Report, you submit a protocol with a detailed study design and plan, which is then reviewed by an editorial board, often suggestions for improvement are made, and if accepted on re-submission, the journal, within reason, commits to publishing your study irrespective of whether your findings are statistically significant.

Following on this model, Assignment 3 will be your detailed study design plan. Your TA will be your peer reviewer as they grade your submission. Assignment 4 will be your re-submission of your study design based on feedback from your TA. This will be followed by your final in class presentation of the results of your proposed study!

To prepare you for this, we’ll start with a short review of materials related to Open Science, R, & RMarkdown from BIOL 125. After reviewing this material, you should be set to draft your protocol using an RMarkdown template.