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	McElreath, Richard. 2020. Science as Amateur Software Development. https://www.youtube.com/watch?v=zwRdO9_GGhY. Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. 2017. “Good Enough Practices in Scientific Computing.” PLOS Computational Biology 13 (6): e1005510. https://doi.org/10.1371/journal.pcbi.1005510.
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.	Lab 1: Git
3	Sep 06	Fundamental techniques: Debugging errors and getting help	“R Faq - How to Make a Great R Reproducible Example.” n.d. Stack Overflow. Accessed August 31, 2018. https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example. Bryan, Jenny. 2020. “Object of Type ‘Closure’ Is Not Subsettable.” Presented at the RSTUDIO::CONF 2020, January 31. https://rstudio.com/resources/rstudioconf-2020/object-of-type-closure-is-not-subsettable/. Wickham, Hadley. 2019. “Debugging.” In Advanced R, Second Edition, chap. 22. CRC Press. https://adv-r.hadley.nz/debugging.html.	Lab 2: Debugging
4	Sep 13	Fundamental techniques: Programming paradigms	Introduction to the "Functional Programming" section of Advanced R: https://adv-r.hadley.nz/fp.html Introduction to the "Object-oriented Programming" section of Advanced R: https://adv-r.hadley.nz/oo.html Chambers, John M. 2014. “Object-Oriented Programming, Functional Programming and R.” Statistical Science 29 (2): 167–80. https://doi.org/10.1214/13-STS452. (Non-paywalled copy)	Lab 3: Programming paradigms
5	Sep 20	Data journeys (Covid contrarianism I)	Bates, Jo, Yu-Wei Lin, and Paula Goodale. 2016. “Data Journeys: Capturing the Socio-Material Constitution of Data Objects and Flows.” Big Data & Society 3 (2): 2053951716654502. https://doi.org/10.1177/2053951716654502. Madrigal, Robinson Meyer, Alexis C. 2021. “Why the Pandemic Experts Failed.” The Atlantic. March 15, 2021. https://www.theatlantic.com/science/archive/2021/03/americas-coronavirus-catastrophe-began-with-data/618287/. Banco, Erin. 2021. “Inside America’s Covid-Reporting Breakdown.” POLITICO. August 15, 2021. https://www.politico.com/news/2021/08/15/inside-americas-covid-data-gap-502565.	Project: Proposal
Exploratory data analysis
6	Sep 27	EDA	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	EDA	No new readings	Lab 4: EDA
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.	Project: Data Journey Narrative
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.	Lab 5: Code Review
11	Nov 01	Work week	No new reading In-class time to work on labs and projects	Lab 6: Reproducibility
12	Nov 08	No class: Election Day & Instructor at conference		Project: EDA
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	Project: Code Review
16	Dec 06	Covid contrarianism III	Leonelli, Sabina. 2021. “Data Science in Times of Pan(Dem)Ic.” Harvard Data Science Review, January. https://doi.org/10.1162/99608f92.fbb1bdd6. Johnson, Kaneesha R. 2021. "Two Regimes of Prison Data Collection." Harvard Data Science Review, Summer. https://doi.org/10.1162/99608f92.72825001 Optional: Rodriguez-Lonebear, Desi. 2016. “Building a Data Revolution in Indian Country.” In Indigenous Data Sovereignty, edited by Tahu Kukutai and John Taylor, 1st ed. ANU Press. https://doi.org/10.22459/CAEPR38.11.2016.14.
	Dec 13	Project presentations (9:30am, GRAN 120) Hard deadline for everything		Project: Report & Presentation