FISH 6002 Syllabus

Data Collection, Management, and Display

  • Instructor: Dr. Brett Favaro
  • Classroom: W3033/35
  • Times: Mondays 1500-1700, Tuesdays 0900-1000
  • Office Hours: Thursday 0900-1200, W2009

Modern fisheries scientists work in a complex data environment. This course will introduce students to the basics of R statistical software - including programming best-practices, optimizing workflows, and producing tidy data. A focus on data display and visualization will be present throughout this course, reflecting the importance of good graphing habits in science.

Learning Outcomes

By the end of this course, students will develop a working competency of R Statistical Software, and will be introduced to the software environment that fisheries scientists must master. Great importance will be placed on fostering the ability to self-teach and stay abreast of developments in data collection, management, display, and programming.

Students will also develop the following specific competencies:

Data collection

  • Understand the wide diversity of data that one may collect within fisheries science
  • Understand “Tidy data”
    • How to collect it
    • How keeping data tidy helps with analysis
    • How to clean up untidy data in a reproducible, transparent way (especially using dplyr)
  • Familiarity with best practices in recording data in the field, and preventing loss between collection and analysis

Data management

  • Understand metadata, archiving, and how to build an efficient project workflow
  • Able to create and implement a data management plan
  • Understand how to manipulate data and prepare it for analysis
    • Focus: dplyr
  • Understand the difference between open, community-supported software, and conventional licensed software
  • Able to produce reproducible, well-documented R code
  • Understand the concept of open data

Data display

  • Able to communicate data visually, selecting the appropriate figure to represent data
  • Familiarity with both R base plots and the ggplot2 ecosystem
  • Demonstrated ability to produce effective graphs for:
    • Scientific posters
    • Scientific publications
    • Powerpoint-based talks
  • Ability to produce figures that meet journal standards for publication

Workflow and security

  • Understand how to ask questions using minimal reproducible examples
  • Use R Studio’s project management tools to follow an efficient workflow
  • Understand how to apply basic security steps to protect your data and identity

Expectations and Aspirations

Look, I get it - very few people go into fisheries or biological sciences because they want to program all day long. But the reality is that computer competency is a core skill - just like reading and writing - for the modern scientist, and you are no different. But if you build these skills early on, then you will actually spend less time overall struggling to make your way throught the digital landscape of science.

My goal for you is to emerge with two skillsets. First: the ability to efficiently collect, store, and prepare data for analysis and display Second: To be able to create beautiful and effective visual depictions of data using R and the ggplot2 package.

My expectation is that if this is all new to you, that you keep up with the course and seek help proactively when needed. If you’re more advanced, my hope is that you share your knowledge with the rest of the class, so that we can all become more effective at these critical skills needed to succeed in science.

Course Structure

The course will meet twice weekly - one 2-hr block and one 1-hr block. Speaking generally, we will spend about 1 hour of lecture introducing the theory behind the week’s activities. The remaining two hours will be spent on how to actually use this knowledge in the conduct of research.

Reference Books

The Internet is awash in information on the subject matter covered by this course. The following books and papers are excellent references. You don’t need to buy them all, but you should certainly look at all of them at some point during your research career.

The Tufte books are timeless references for data display theory. The Wickham books and articles are constantly evolving as the software changes, but represent great starting places.

Essentially, our theory will follow Tufte, and our practice will derive from Wickham. In some cases, full text of the books may be available online for free.

Tufte, Edward R. (1986). The visual display of quantitative information , p. 200. ISBN: 978-0961392147.

Tufte, Edward R. (1990). Envisioning information. New York: Graphics Press, p. 126.

Tufte, Edward R. (1997). Visual explanations: images and quantiles, evidence, and narrative , p. 157. ISBN: 02768739. DOI: 10.1109/TPC.1998.678564.

Tufte, Edward R. (2006). Beautiful evidence. New York: Graphics Press LLC, p. 213. ISBN: 0961392177.

Wickham, Hadley (2014). “Tidy data”. In: Journal of Statistical Software 59.1, pp. 1–23. DOI: 10.18637/jss.v059.i10.

Wickham, Hadley (2016). ggplot2: elegant graphics for data analysis (use R!) 2nd ed. 2016 edition. Springer, p. 260. ISBN: 978-1491910399. http://ggplot2.org/book/.

Wickham, Hadley and Garrett Grolemund (2017). R for data science: visualize, model, transform, tidy, and import data. O’Reilly Media, p. 518. ISBN: 978-1491910399. http://r4ds.had.co.nz/index.html.

Xie, Yihui (2018). Bookdown: Authoring books and technical documents with R Markdown. https://bookdown.org/yihui/bookdown/

Course Policies

Social Media

I use the hashtag #MIData on Twitter to highlight content that may be of interest to this course. I encourage using Twitter and other social platforms to communicate your work.

However, I want people in the class to feel comfortable pushing themselves in a supportive environment. To that end, I ask that students not tweet out content from our lectures - including things said by myself or classmates, or pictures or video of our class activities. My goal is for us to learn together, and having someone recording, tweeting, etc. the contents of discussions as they progress can be stifling.

If you wish to tweet more generally (e.g. “Learning about tidy data today in #MIData” that is acceptable).

Code of Conduct

You have the right to expect a supportive, safe environment in this course. This course will be governed by my Fisheries Science Code of Conduct, which all participants are expected to respect.

Digital Competency

Students are expected to have basic computer competency. You should be able to operate Microsoft Word, Powerpoint, and Excel, or equivalent (e.g. OpenOffice or Google Docs). You should be able to download and install software onto your computer. Please install R Statistical Software and RStudio prior to begining the course.

If you lack these skills, please consult training materials on your own time. Please bring a laptop to every class.

E-mail Policy

E-mail is not a primary tool for communication in this class. If you have questions about course content, your order of operation should be:

  1. Check the syllabus
  2. Ask in class, or discuss with colleagues
  3. Ask on Slack (this way, everyone can benefit from an answer)
  4. Request a meeting with me

If emailing me a meeting request, use the subject line “FISH 6002: Meeting request.” Please indicate three potential meeting times (I prefer afternoon meetings) and explain in 1-3 lines what you want to meet about.

E-mail is impersonal, burdeonsome, and adds to confusion.

Class Participation

There will be a LOT going on in this class. Most assignments are designed to be completed mostly in-class time. The class is highly collaborative, meaning you need to be present to do it.

Accomodations will be made for serious illness or other extenuating circumstances. However, it is the student’s responsibility to stay caught up with course materials - and missing in-class activities will result in a decreased participation grade.

So please, don’t make it part of your plan to miss class!

Academic Honesty

This course is governed by MUN’s regulations on academic misconduct.

Course Schedule

Week 1: Data and Software in Fisheries

Week 2: Introduction to R

Week 3: Markdown and RStudio workflow

Week 4: Intro to Tidy Data

Week 5: Visual Display of Data 1

Week 6: Visual Display of Data 2

Week 7: Working with Messy Data

Week 8: Collecting and Managing Tidy Data

Week 9: Visual Display of Data 3

Week 10: Figures for Science Communication

Week 11: Maps

Week 12: Interactive Plots

Assignments and Grading

See assignment guide for details.

10% Participation

30% Minor Assignments

60% Major Assignment