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Introduction to R and RStudio for BMI 510 Course

Learn how to install R and RStudio for the BMI 510 course, explore the resources available, and understand the grading structure. Utilize Hadley Wickham's tutorials to enhance your R programming skills. Get ready for the upcoming Journal Club presentation and statistics discussions. Stay updated with course materials and assignments submission guidelines.

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Introduction to R and RStudio for BMI 510 Course

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  1. BMI 510: R/RStudio installation J. Lucas McKay, Ph.D., M.S.C.R. Departments of Biomedical Informatics and Neurology, Emory University, Atlanta, GA USA Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA

  2. We will use R and RStudio in this class • • R is the language, RStudio is the development environment. Installing R: • Windows • https://cran.r-project.org/bin/windows/base/ • OS X • https://cran.r-project.org/bin/macosx/ Installing RStudio: • https://posit.co/download/rstudio-desktop/ Common extensions are available with this command within RStudio • install.packages("tidyverse") Check installation: • library(tidyverse) • ggplot(mtcars,aes(cyl,mpg)) + geom_point() • • •

  3. Please take a few minutes and install R and RStudio You may use VSCode/Similar as a frontend as you like, but assignments will be returned in .Rmd format

  4. R resources • R has a fantastic open source community and didactic resources. In the last few years, adoption has been rapidly accelerated by the contributions of Hadley Wickham, the creator of ggplot2 and currently the chief scientific officer of RStudio • His tutorials on R are very accessible and a quick read: • R for Data Science • The exercises are quick and ‘’ fun ‘’

  5. Course grading • • • • • Weekly homework Journal club presentation Quiz 1 Quiz 2 Final software package 30 % 10 % 20 % 20 % 20 %

  6. Role of programming in course • We will use R in this course, but the techniques are general and could be performed in python or compiled languages. • We will do a considerable amount of computer simulation, and assume students have basic knowledge of scientific computing prior to course entry.

  7. How to turn in work • We will use functionality in the REDCap clinical data management tool to turn in work this year, as well as to do surveys and things like that. • Most assignments will have a template R Markdown File (.Rmd) with the problems. You fill in the code and upload the file. • All assignments are due at 5 PM on Mondays. • Late assignments: 2% of the assignment’s total points will be deducted for every hour it is late. • Extensions: if you are on medical service, or need other accommodations let the instructor know. Extensions cannot be granted after work is assigned.

  8. How to access course materials • We will email out a finalized syllabus this afternoon. Any updates will be emailed out. • Lecture recordings and slides will be posted on Dr. McKay’s website at https://jlucasmckay.bmi.emory.edu/global/bmi510/.

  9. Other topics for today • Complete your student information survey, please. • If you are unfamiliar with R, please spend some time with the Wickham tutorials. This will make the actual programming exercises much easier. • Homework Zero will be emailed out shortly. This is a very straightforward exercise. If you do not like it, consider whether BMI 510 is the most efficient way for you to access this material.

  10. Tomorrow and Monday • Tomorrow we will introduce the Journal Club component of the course. • Monday, we will begin talking about statistics. • Homework zero is due at 5 PM Monday.

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