Analyze health data from the Apple Watch

Being #extra at my doctor’s appointment
apple watch

Lindsay Lee


March 30, 2024

I have a doctor’s appointment soon, and I wanted to see if health data from my Apple Watch could help inform our conversation. The Health app has interesting visualizations out of the box, but I wanted to do something a tad more complicated.

To download the data from the Apple Health app on your iPhone, go to the Health app, click on your profile picture in the top right corner, and select “Export All Health Data”. This will create a zip file that you can share with yourself. Next download the zip file and extract the contents. The important file in this extract is export.xml. I have this file saved in a folder data/apple_health_export in my GitHub repository. I have the data folder in the .gitignore file so that the data is not uploaded to this GitHub repository.

It’s not super easy to work with the data in xml format, so I wanted to convert this data to csv format. Luckily I found someone else’s code to do exactly this. I saved their parsing function as in my GitHub repository for this analysis.

To see the xml data as json within the terminal, run the following command in the Terminal:

python data/apple_health_export/export.xml

To convert the xml data to a csv file, run the following command in the Terminal:

python data/apple_health_export/export.xml | jq -r '[.startDate, .endDate, .type, .unit, .value] | @csv' > data/apple_health_export/export.csv

This requires the JSON parser jq to be installed. I installed jq via Homebrew on my Mac with: brew install jq.

With the data in a usable format, it’s easy to make all kinds of nice graphs. I have a couple examples in my script print_spo2_graph.R in the repository. The pdf output is saved to an output folder which is also in .gitignore (sorry, nosy nellies!)

Now I’m all ready for my appointment. I’m sure my doctor will think this is useful and not a waste of everyone’s time.