APHREA: Getting Started

Transcript

1. 1 GETTING STARTED Jeff Goldsmith, PhD Department of Biostatistics
2. 2 • The short course is intended to introduce some common tools • This lecture will get us started by focusing on: – RStudio – Some coding best practices – R Markdown – Project organization Overall goals
3. 3 • Makes life much easier for useRs (not a typo – people who use R are sometimes referred to as useRs…) • The RStudio folks are also leading the development of a new analytic framework within R, and that work is integrated into RStudio Why are we using RStudio?
4. 4 • Rstudio is an Integrated Development Environment (IDE) – It’s got everything you need to do data science in R – This IDE is one of the better reasons to use R … Working in RStudio
5. 4 • Rstudio is an Integrated Development Environment (IDE) – It’s got everything you need to do data science in R – This IDE is one of the better reasons to use R … Working in RStudio R for Data Science
6. 5 • Code is case sensitive • There is no autocorrect • Establish a variable naming convention – this_is_snake_case – this.is.period.case – thisIsLowerCamelCase – ThisIsUpperCamelCase • Your names should match your regex skills • Extensive documentation will save you headache Code
7. 6 • Treat your inputs (e.g. raw data) and code as “real” – Your results and created by input and code, and you can always reproduce your results from these if you need to • Your code matters – It’s one of the most central ways you will communicate. • Plan for mistakes – Write code that makes it easy to fix mistakes without breaking the rest of your analysis Some perspective on code
8. 6 • Treat your inputs (e.g. raw data) and code as “real” – Your results and created by input and code, and you can always reproduce your results from these if you need to • Your code matters – It’s one of the most central ways you will communicate. • Plan for mistakes – Write code that makes it easy to fix mistakes without breaking the rest of your analysis Some perspective on code
9. 7 • You spend a lot of your time communicating in writing – With collaborators, a general public, future you – About data cleaning, analyses, results – In formal reports, brief summaries, replies to questions Text and code are important
10. 8 • Code is necessary but not sufficient for clear communication • Use tools that combine your code and text • Greatly facilitates reproducibility, which is a big concept – In short, someone you don’t know or work with should be able to reproduce each step of your analysis – As a part of this, they should understand why you did what you did – (Again, this someone is often future you) • We’ll use R Markdown to write reproducible reports Tools
11. 9 • A “Markdown” language is a lightweight syntax that can be easily converted to another format (HTML, PDF, Word) • R Markdown lets you combine formatted text with code chunks and the results of those chunks • Having text and code in the same place, and having the combined output be user-friendly, is huge for your workflow R Markdown R for Data Science
12. 9 • A “Markdown” language is a lightweight syntax that can be easily converted to another format (HTML, PDF, Word) • R Markdown lets you combine formatted text with code chunks and the results of those chunks • Having text and code in the same place, and having the combined output be user-friendly, is huge for your workflow R Markdown R for Data Science
13. 10 Organizing files
14. 10 Organizing files
15. 10 Organizing files
16. 11 Being organized will frequently make your life easier • “Your most frequent collaborator is you from six months ago, but you don’t reply to emails”1 • Eventually, someone other than you (or even future you) will need to reproduce your results – Be ready for that. Why organization matters 1. This version of the quote comes from Karl Broman, who traced it to a tweet: http://bit.ly/motivate_git
17. 12 Time to code!!