https://github.com/trangdata/phase2.1neurorpackage
https://github.com/trangdata/phase2.1neurorpackage
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/trangdata/phase2.1neurorpackage
- Owner: trangdata
- License: other
- Created: 2021-01-18T17:21:10.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2021-01-20T17:19:59.000Z (over 5 years ago)
- Last Synced: 2025-01-13T01:34:48.640Z (over 1 year ago)
- Language: R
- Size: 32.2 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
title: "Analysis of COVID-19 patients with Neurological Conditions"
output: rmarkdown::github_document
---
[](https://github.com/trang1618/treeheatr/actions)
```{r, include = FALSE}
knitr::opts_chunk$set(
fig.path = "man/figures/"
)
```
## Install
You can install the development version of **Phase2.1NeuroRPackage** from GitHub with remotes:
```{r, eval=FALSE}
# install.packages('remotes') # uncomment to install devtools
remotes::install_github('covidclinical/Phase2.1NeuroRPackage')
```
## How to run
The main function `runAnalysis()` has 6 arguments.
Please read the documentation with `?runAnalysis` for a detailed explanation.
```{r}
library(Phase2.1NeuroRPackage)
runAnalysis(mysite = 'penn', mask_thres = 10, blur_abs = 0, include_race = TRUE,
out_dir = 'output', data_dir = '../thrombotic-penn/data')
```
See your site obfuscation parameters (`mask_thres` and `blur_abs`) [here](https://docs.google.com/spreadsheets/d/1Xl9juDBXt86P3xQtsoTaBl2zPl1BIiAG9DI3Rotyqp8/edit#gid=212461777).
If your site does not have race information, set `include_race = FALSE`.
Please submit the results to the central repository:
```{r, eval=FALSE}
FourCePhase2.1AKI::submitAnalysis()
```
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/covidclinical/Phase2.1NeuroRPackage/issues/new).
Thank you very much for your support!