Readings: Week 4
Week 4: Reproducible data (re)organization
Objectives and Competencies for this session:
- Understand and be able to explain the importance of a well-documented, reproducible workflow
- Be able to outline a logical workflow for data importing and correction
- Be able to load a file as a dataframe in RStudio, edit the data frame, and save the corrected version as a csv file
Pre-Class Preparation:
Readings:
Read 1-3 before class. #4 goes into more more detail than is necessary before class, but I include it because it will be more useful as you become more experienced.
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Laskowski, 2020. What to do when you don’t trust your data anymore. [read online] or [download pdf]
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Pennisi, E. 2020. Spider biologist denies suspicions of widespread data fraud in his animal personality research. Science. [read online] or [download pdf]
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Alston, J. M., and Rick, J. A.. 2020. A Beginner’s Guide to Conducting Reproducible Research. Bull Ecol Soc Am 00( 00):e01801. [read online] or [download pdf]
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Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK (2017) Good enough practices in scientific computing. PLoS Comput Biol 13(6): e1005510. [read online] or [download pdf]
Videos:
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A Data Sharing and Management Snafu in 3 Short Acts, by the NYU Health Sciences Library
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These introductions to R and R Studio were made by Professor Ethan White (UF-WEC). They are a good overview of some R basics. Although we will cover these topics in class, going through them before class would be useful.
Reminder: Don’t forget to install the Tidyverse library; you can read how on this page. And if you want to get ahead to what we will be doing in class, you can read about how to Set up a Project in R
Note: Computer programming can be challenging (or frustrating) to learn and teach. The next few sessions we will be using modified version of a style known as:
(1) I do it
(2) We do it
(3) You do it
This means you first observe me doing something in Rstudio by watching a video (or in this case you’ll watch a video of Prof. Ethan White). The in class we will do some tasks together at the same time (aka “live-coding”). This is useful, because you can ask questions as you go. Then, you will work on an assignment based on the tasks we did together, which you will submit as your assignment.