To prepare to follow along, you will need to have the datasets downloaded, some spreadsheet program (e.g., Excel), and a programming language (e.g., R) installed. See the below sections for how to get everything set up
You can find all the datasets needed from the workshop from the book’s GitHub Page:
You can click on the “Code” dropdown and select “Download Zip” to download the data and files for the lesson materials.
Microsoft Excel and Google Sheets are the more common types of spreadsheet software used. If you do not have Excel, there are other free options availiable:
- LibreOffice (Free and open source): https://www.libreoffice.org/
- FreeOffice (Free but closed source): https://www.freeoffice.com/en/
All of these programs can read and write Excel and comma delineated (CSV) files, which you can use to follow along.
Below you will find the installation instructions for setting up the programming language we will be using (e.g., R) along with its programming environment (e.g., RStudio)
We will be using R and RStudio for the workshop. If you would like a video installation tutorial, please see the R section of The Carpentries workshop template .
The links to install R can be found here: https://cloud.r-project.org/. Navigate to the correct operating system.
For mac users, download the
.pkg file under the “Latest release” section
For Windows users, please install both the
base version as well as
After you have installed R, you can install RStudio. We will use RStudio as the integrated development environment (IDE) to write and work with R code. Rstudio can be downloaded from the following location: https://rstudio.com/products/rstudio/download/
Installing R packages
Once we have Within RStudio, there will be a “Packages” tab in the bottom right panel. Click on the “Install” button.
In the pop-up window type in “tidyverse” and click “install.”
The Console section of RStudio will begin installing the “tidyverse” package we will be using.
Testing your installation
When the installation is finished, you can check if the package was installed properly and will load by scrolling down the “Packages” tab and clicking the checkbox next to “tidyverse.”
You can click one of the Binder badges to launch a programming environment for you in the cloud.
R + RStudio
You may click one of the RStudio Binder badges to launch an RStudio instance.
- RStudio (complete):
- This may take a longer time to load, but everything should be set up.
- RStudio (partial):
- This may take less time to load, but you need to install some more packages on your own and download the lesson datasets.
To setup the partial RStudio environment, you need to run the following commands in the bottom left “Console” panel.
Then type the following to install the
medicaldata package for some of the medical datasets we will be using.
To download the data files go to the top right corner and click the
Project (None) drop down,
Version Control >
Git and paste in
https://github.com/chendaniely/ds4biomed.git for the
You can leave the rest of the parameters as their defaults,
and then click
When this process finishes,
the bottom right quadrant’s “File” tab should show the
ds4biomed folder and you should see the
data folder listed.