This week, we will cover Rmarkdown and talk about how it can be used to create reproducible data-focused protocols.
For Monday, please read the following two modules:
- Introduction to reproducible data pre-processing protocols
- RMarkdown for creating reproducible data pre-processing protocols
For Wednesday, please read one additional module, as well as an example of a data-focused protocol:
You can click here to download the slides for the lecture this week.
Due: Feb. 9
For this week's assignment, you will be replicating the data processing example shown in the example protocol from the reading.
- Read in data from the example and perform pre-processing on it. This file is available as a CSV file here. You can either use "Save As" in your web browser's menu bar to save this file as a CSV, or you can copy all the text on the page and paste it into a plain text file on your computer. Whichever method you use, please make sure you've named the file "cfu_data.csv". Perform the same analysis that is shown in the protocol on these data. This should not require you to create any new code, only copy and run code in the protocol, but please take a look at the code as you run it to see if you understand how each part of the data processing works. You should be able to recreate the output dataset from the example protocol.
- Address a “what if we looked at the data this way instead” question with a prediction. How would you need to change the code from part 1 if the data were saved in a file with a different name? How would you need to change the code if data were collected for several more experimental groups (and so the starting data had more rows)? As a challenge question, how would you need to change the code if the plating method in your laboratory changed to use a full petri dish to plate each sample, rather than a quarter of a petri dish, as shown in the example?
- Describe the R package/library presented in class and what innovation it provides. Describe briefly how Rmarkdown can be used to create reproducible data-focused protocols. What are the advantages of using Rmarkdown for this rather than a word processing program (e.g., Word)?
Please submit an R script for part 1, with the code you used to reproduce the results in the example protocol. Please use Rmarkdown to write up your answers to parts 2 and 3 (nicely formatted, please!) and render that to a Word or PDF document to submit.