As the paper looks overall complete, below are some suggestions and comments that I can give:
Good job separating the commits using meaningful names.
The folders are all updated clearly with an informative Readme
Good name for the repository
Paper:
For the data section, it would be nice to address the groups with income level of NA, what are the possible causes and how you chose to dealt with it, as there seems to be fairly high amount of NAs.
It would be helpful to include information about the sample size, demographic characteristics, and any potential biases in the dataset.
Can consider including more recent references if any other sources are relevant.
Can consider resizing some of the figures to help readers read it easily
Well down on your current progress!
As the paper looks overall complete, below are some suggestions and comments that I can give:
Paper:
Good luck!