This is a five hour computing bootcamp for incoming Ph.D. and M.S. students to the Department of Statistical Science at Duke University. These materials are adapted from the 2018 bootcamp by Mine Çetinkaya-Rundel and Colin Rundel.
The workshop will cover the following topics:
- Account activation and access to departmental servers
- Discussion of how to responsibly use distributed computing resources
- Docker containers and Duke VM
- RStudio
- Jupyter Notebook
- Recognize the problems that reproducible research helps address, featuring a brief discussion of case studies gone wrong and how reproducible research could have possibly helped
- Identify pain points in getting your analysis to be reproducible
- The role of documentation, sharing, automation, and organization in making your research more reproducible
- Introduce some tools to solve these problems, specifically R / RStudio / R Markdown
- Organize projects and folders to enable reproducibility and reusability
- Understand the structure of data files and the importance of documenting all changes made
- Create a reproducible project workflow using R / RStudio / R Markdown
- Introduce git and GitHub.
- Initiate a project directory, understand the git workflow, and create a pull request to a remote repository
- Discuss the role of version control in reproducibility
- Discuss version control best practices
- Navigate R Markdown and RStudio
- Analyze data and create graphics with package tidyverse
- Discuss workflow
- Navigate Jupyter notebooks
- Introduce Python basics, control flow, and functions
- Discuss popular Python packages including: NumPy, SciPy, pandas, matplotlib, seaborn, scikit-learn, and TensorFlow
- Discuss similarities and differences between Python and R
- Discuss how to leverage the best of R and Python
- Department of Statistical Science Computing Bootcamp 2018 by Mine Çetinkaya-Rundel and Colin Rundel
- Retraction Watch
- A Byte of Python by Swaroop C H
- Jupyter
- Python
- Python Crash Course by Eric Matthes
- R for Data Science by Hadley Wickham and Garret Grolemund