R code to run, validate, and submit the analysis for the SeverityAug project.
To install this package in R:
devtools::install_github("https://github.com/covidclinical/Phase2.1SeverityAugRPackage", subdir="FourCePhase2.1SeverityAug", upgrade=FALSE)
To run, use the following command:
FourCePhase2.1SeverityAug::runAnalysis(chartReview_path = 'YOUR PATH HERE', maxdays = 30, mindays = -2, outcome = 'Severe?')
FourCePhase2.1SeverityAug::submitAnalysis()
The runAnalysis function has 4 arguments:
-
chartReview_path: location of chart-review data
-
maxdays: maximum length of admissions to consider (default value: 30)
-
mindays: days prior to admission from which to collect events (default value: -2)
-
outcome: one of "Severe?" or "COVID-19 Hospitalization?"
The chart-review data should be a comma delimited file with 3 columns: "patient_num", "COVID-19 Hospitalization?", and "Severe?"
The latter 2 columns should be binary 1/0 based on the chart reviewed assessment of the patient admission.
| patient_num | COVID-19 Hospitalization? | Severe? |
|---|---|---|
| 231 | 1 | 1 |
| 542 | 1 | 0 |