Each participants should prior to the course:
- Complete Datacamp courses Introduction and Intermediate R. If you have not yet received an invitation please contact us!
- Install in the newest(!) version:
- Get accounts for:
- Github You can have the academic version with Charité email
- RStudio Cloud You can login via the Github credentials
Important resources to use if you do not know how to proceed/need help:
- Cheat sheets on different packages like tidyverse/ggplot, etc.
- Stackoverflow A community of nerds at your disposal. All beginners questions have been already posted so a simple search is enough!
- help function in R (put cursor on function name and press F1 or type ?function_name)
- at the end of each help text there is a so called vignette that will give an executable example so that you can experiment with the function and its outputs
- contact us. We will explain rules for our online classes in the first session.
We will meet on Fridays in an online format. We will use a video confercing software. Each course will consist of a short lecture on issues in reproducibility in research, an introduction to a specific topic in programming with R, and an exercise.
- Pre course work: Course work on Datacamp (Introduction and Intermediate R)
- 24.04.Preregstration, Intro to RStudio Cloud and R (have the Base R Cheat Sheet ready) I) Exercise: Functions II) Homework: Play around with RCloud and your own RStudio instance on your computer
- 15.05. Data management I) Exercise: Vectorisation II) Homework: tidyverse on Datacamp; Read: https://doi.org/10.1038/s41598-018-27482-2
- 22.05.Tidyverse I) Exercise: tidyverse II) Homework: ggplot2 part 1 on Datacamp; Read: https://doi.org/10.1371/journal.pone.0185195
- 29.05. Advanced Plotting I) Exercise: ggplot II) Homework: course of your choice on Datacamp
- 05.06. Linear Models I) Exercise: linear_models II) Homework: course of your choice on Datacamp
- 12.06. Linear Mixed Models I) Exercise: linear_mixed_models II) Homework: Read through the tutorial for Git/Github
- Hackathon (One Saturday tbd) I) Exercise: Git and Github II) Bring your own small problem, we will work on it in small groups
- 19.06. Reproducible Research from planning to publication
This course will be taught online only and with that come some challenges. In the first session we will try to resolve as many as possible. We will use the Charité instance of MS teams as our platform for video meetings. All code will be provided on Github where also this document here resides. Additionally, an OSF project will contain all presentations and a link to the Github repository.
Each session will begin with a 20 Minute Presentation on issues of reproducibility (see Course Program). After this, there will be a short introduction to R functionalities needed in the upcoming exercise. The exercise itself will be done online in the RStudio cloud. This allows us to run all the exercises without the need to install everything locally on your computer. You are encouraged, however, to also do the same things locally on your computer. Please bear in mind that you need to install all libraries prior to using them
install.packages("tidyverse")
library(tidyverse)
The installation has to be done only once. The library has to be loaded each time R is restarted. It is good practice to load the libraries at the start of the script where they are used.
I will invite you to RStudio Cloud before the course, you need an account however (see Preparation). When the course starts we will the clone the course project to your project folder. All libraries are preinstalled. Each folder in the project is one course day. You will need to work on the exercise file. Only resort to the solution file after the course day. The exercise is that you try to solve this on your own (with our help) and not just copy paste a solution.