Chapter 7 Resources

7.1 (blogs, sites, books, courses):

• Matthew Shotwell’s slides (2011): “Approaches and Barriers to Reproducible Practices in Biostatistics”
• NIH Training Module: Reproducibility through rigor and transparency
• Gandrud, Christopher. Reproducible Research with R and R Studio, CRC Press, 2013.
• Xie, Yihui. Dynamic Documents with R and knitr, Vol. 29. CRC Press, 2013.
• ROpenSci’s blog post: “Reproducible research is still a challenge”, by R. FitzJohn, M. Pennell, A. Zanne, W. Cornwell, June 9, 2014
• Karl Broman’s class “Tools for Reproducible Research” at UWisconsin-Madison.
• “Reproducible Research” by Johns Hopkins on Coursera (Peng, Leek, Caffo)
• Stodden, Victoria, Friedrich Leisch, and Roger D. Peng, eds. Implementing reproducible research, CRC Press, 2014.
• StackOverflow question “Why should I use version control?”
• Learn git on github: link
• Reproducible research with R and RStudio: http://christophergandrud.github.io/RepResR-RStudio/
• Tools for reproducible research: https://kbroman.org/Tools4RR/
• Data privacy and security: https://dataprivacymanager.net/security-vs-privacy/
• BC-Gov framework for github https://github.com/bcgov/BC-Policy-Framework-For-GitHub
• Making slides with Xaringan package in RMarkdown: https://arm.rbind.io/slides/xaringan.html
• Data wrangling with R: https://cengel.github.io/R-data-wrangling/
• Data cleaning with R and tidyverse: https://towardsdatascience.com/data-cleaning-with-r-and-the-tidyverse-detecting-missing-values-ea23c519bc62
• Gallery of missing data visualization: https://cran.r-project.org/web/packages/naniar/vignettes/naniar-visualisation.html
• How does R handle missing values: https://stats.idre.ucla.edu/r/faq/how-does-r-handle-missing-values/
• What does research reproducibility mean? https://stm.sciencemag.org/content/8/341/341ps12
• Challenge to scientists: does your ten-year-old code still run? https://www.nature.com/articles/d41586-020-02462-7?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature#ref-CR1
• Reproducible Research and open science: https://ropensci.github.io/reproducibility-guide/sections/introduction/

7.2 Participant polls