4CE Phase 2.1 Neurological Condition Analysis
This repository performs missing data analysis on data at different sites and reports the results in the results/ folder.
Which script should I run?
Short answer: elix-short-term.Rmd and elix-cpns.Rmd
The best way to run this analysis is to clone this repository on your local machine (please ensure you're in a directory where you want the repository to be downloaded):
git clone https://github.com/trang1618/neuro-penn.git
Then, go inside the repository:
cd neuro-penn
and make a copy of elix-short-term.Rmd, name it with your site name, for example:
cp elix-short-term.Rmd elix-short-term-penn.Rmd
Then, open the R project
open neuro-penn.Rproj
and navigate to the newly created file (e.g. elix-short-term-penn.Rmd) to modify the code to run on the data at your specific site.
Please be sure to change the second code chunk to read in your site-specific data, including replacing "penn" with your site name, for example, mysite = 'nwu'.
Once everything runs, please hit the "Knit" button on top of the .Rmd file to create an .html file that will automatically be put into htmls/.
Knit the elix-cpns-[your_site_id].Rmd similarly.
Finally, please upload your results (in results/ and htmls/) via a pull request or request @trang1618 to add you as a contributor.
If you run into any problem adapting this code to your data, let us (@meghutch and @trang1618) know via Slack or submit an issue.
Troubleshooting
Where is the run_fish() function?
It's under R/run_fish.R.
We also have other utility functions in the R/ directory.
If you did not clone the repo, you can simply download these files in the R/ directory and source them in the main notebook.