https://github.com/trangdata/neuro-penn
https://github.com/trangdata/neuro-penn
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/trangdata/neuro-penn
- Owner: trangdata
- Created: 2020-11-03T15:24:57.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2021-01-28T15:16:24.000Z (over 5 years ago)
- Last Synced: 2025-03-02T13:27:54.122Z (over 1 year ago)
- Language: HTML
- Size: 25.9 MB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: readme.md
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README
# 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/`](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/`](htmls/).
Knit the `elix-cpns-[your_site_id].Rmd` similarly.
Finally, please upload your results (in [`results/`](results/) and [`htmls/`](htmls/)) via a [pull request](https://github.com/trang1618/neuro-penn/pulls) 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](https://github.com/trang1618/neuro-penn/issues/new).
## Troubleshooting
### Where is the `run_fish()` function?
It's under [`R/run_fish.R`](R/run_fish.R).
We also have other utility functions in the [`R/`](R/) directory.
If you did not clone the repo, you can simply download these files in the [`R/`](R/) directory and source them in the main notebook.