Fall 2022
UC Merced
Prof. Dan Hicks (they/them)
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GRAN 120
TÞ 12:00-1:15pm

week date topic readings assignment
Some fundamental tools
1 Aug 25

Motivation: What researchers can learn from software engineering

2 Aug 30

Fundamental tools: git, tests, and R Markdown

  • Ram, Karthik. 2013. “Git Can Facilitate Greater Reproducibility and Increased Transparency in Science.” Source Code for Biology and Medicine 8 (1): 7. https://doi.org/10.1186/1751-0473-8-7.
  • Optional: Blischak, John D., Emily R. Davenport, and Greg Wilson. 2016. “A Quick Introduction to Version Control with Git and GitHub.” PLOS Computational Biology 12 (1): e1004668. https://doi.org/10.1371/journal.pcbi.1004668.
  • Optional: Baumer, Ben, Mine Cetinkaya-Rundel, Andrew Bray, Linda Loi, and Nicholas J. Horton. 2014. “R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics.” ArXiv:1402.1894 [Stat], February. http://arxiv.org/abs/1402.1894.
3 Sep 06

Fundamental techniques: Debugging errors and getting help

4 Sep 13

Fundamental techniques: Programming paradigms

5 Sep 20

Data journeys (Covid contrarianism I)

Exploratory data analysis
6 Sep 27


  • ch. 7, "Phenomena," of Brown, James Robert. 2002. Smoke and Mirrors: How Science Reflects Reality. Routledge. link
  • chs. 2 and 4 of Peng, Roger D., and Elizabeth Matsui. 2016. The Art of Data Science: A Guide for Anyone Who Works with Data. Leanpub. link
  • Huebner, Vach, and le Cessie. 2016. "A Systematic Approach to Initial Data Analysis Is Good Research Practice." The Journal of Thoracic and Cardiovascular Surgery 151 (1): 25-27. https://doi.org/10.1016/j.jtcvs.2015.09.085.
7 Oct 04


No new readings

8 Oct 11

Covid contrarianism II

  • Lee, Crystal, Tanya Yang, Gabrielle Inchoco, Graham M. Jones, and Arvind Satyanarayan. 2021. “Viral Visualizations: How Coronavirus Skeptics Use Orthodox Data Practices to Promote Unorthodox Science Online.” Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems, May, 1–18. https://doi.org/10.1145/3411764.3445211.
  • Douglass, Rex W. 2020. “How to Be Curious Instead of Contrarian About COVID-19: Eight Data Science Lessons From ‘Coronavirus Perspective’ (Epstein 2020).” March 30, 2020. Link.
Reproducibility and replicability
9 Oct 18

The replication crisis

  • Hicks, Dan. 2021. "Open science, the replication crisis, and environmental public health." Accountability in Research. https://doi.org/10.1080/08989621.2021.1962713.
  • Bailey, David H., and Jonathan Borwein (Jon). n.d. “The Reinhart-Rogoff Error – or How Not to Excel at Economics.” The Conversation. Accessed May 15, 2020. Link.
  • Optional: Jager, Leah R., and Jeffrey T. Leek. 2014. “An Estimate of the Science-Wise False Discovery Rate and Application to the Top Medical Literature.” Biostatistics 15 (1): 1–12. https://doi.org/10.1093/biostatistics/kxt007.
  • Optional: Smaldino, Paul, Matthew Adam Turner, and Pablo Andrés Contreras Kallens. 2019. “Open Science and Modified Funding Lotteries Can Impede the Natural Selection of Bad Science.” Royal Society Open Science 6 (7): 190194. https://doi.org/10.1098/rsos.190194.
10 Oct 25

Code review

  • Bryan, Jenny. 2018. “Code Smells and Feels.” Presented at the useR 2018, July 21. https://www.youtube.com/watch?v=7oyiPBjLAWY.
  • Postolovski, Tash. 2020. “Your Code Review Checklist: 14 Things to Include.” July 6, 2020. Link.
  • Buckens, Wouter. 2019. “Self-Documenting Is a Myth, and How to Make Your Code Self-Documenting.” Woubuc. August 3, 2019. Link.
  • Note: We'll be doing code review and trying to reproduce Table 1 from the article below. Read as background, not necessarily for a full understanding.
  • Zhou, Xiaodan, Kevin Josey, Leila Kamareddine, Miah C. Caine, Tianjia Liu, Loretta J. Mickley, Matthew Cooper, and Francesca Dominici. 2021. “Excess of COVID-19 Cases and Deaths Due to Fine Particulate Matter Exposure during the 2020 Wildfires in the United States.” Science Advances 7 (33): eabi8789. https://doi.org/10.1126/sciadv.abi8789.
11 Nov 01

Work week

  • No new reading
  • In-class time to work on labs and projects
12 Nov 08

No class: Election Day & Instructor at conference

13 Nov 15

Project management and sharing data

  • Laskowski, Kate. n.d. “What to Do When You Don’t Trust Your Data Anymore – Laskowski Lab at UC Davis.” Accessed January 29, 2020. Link.
  • caitlinhudon. 2018. “Field Notes: Building Data Dictionaries.” Haystacks (blog). October 30, 2018. https://caitlinhudon.com/2018/10/30/data-dictionaries/.
  • Noble, William Stafford. 2009. “A Quick Guide to Organizing Computational Biology Projects.” PLOS Computational Biology 5 (7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424.
  • Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (1): 1–9. https://doi.org/10.1038/sdata.2016.18.
14 Nov 22

Thanksgiving break

15 Nov 29

Work week

  • No new reading
  • Tuesday: Discuss code review and reproducibility attempt for Zhou et al. (2021)
  • Thursday: In-class work time
16 Dec 06

Covid contrarianism III

Dec 13

Project presentations (9:30am, GRAN 120)
Hard deadline for everything