https://github.com/ctsit/nsofa_calculation
This project provides RScripts to calculate the Neonatal Sequential Organ Failure Assessment score. This project was used as part of a research program at the University of Florida to study neonates.
https://github.com/ctsit/nsofa_calculation
Last synced: over 1 year ago
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This project provides RScripts to calculate the Neonatal Sequential Organ Failure Assessment score. This project was used as part of a research program at the University of Florida to study neonates.
- Host: GitHub
- URL: https://github.com/ctsit/nsofa_calculation
- Owner: ctsit
- License: apache-2.0
- Created: 2020-07-15T13:51:36.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2023-02-10T00:12:49.000Z (over 3 years ago)
- Last Synced: 2025-01-10T14:52:18.230Z (over 1 year ago)
- Language: R
- Size: 140 KB
- Stars: 1
- Watchers: 6
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Authors: AUTHORS.md
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README
# Neonatal Sequential Organ Failure Assessment (nSOFA) Calculation
The nSOFA is an objective, operational definition of organ dysfunction that can successfully identify the risk of mortality among very low birth weight infants with late-onset infection (PMID: 31394566). The nSOFA utilizes categorical scores (total score range 0–15) to objectively describe dynamic changes in: (1) the need for mechanical ventilation and oxygen requirement to maintain a physiologic peripheral saturation (score range 0–8), (2) the need for inotropic support including the use of corticosteroid support (for presumed adrenal insufficiency or catecholamine-resistant shock) (score range 0–4), and (3) the presence and degree of thrombocytopenia (score range 0–3). Medications considered as vasoactive or inotropic included dopamine, dobutamine, epinephrine, norepinephrine, vasopressin, milrinone, and phenylephrine.
## Requirements
The following packages are needed to run the scripts:
tidyverse
vroom
janitor
lubridate
here
openxlsx
readxl
__Note: The dependency management system [renv](https://rstudio.github.io/renv/articles/renv.html) is used to ensure that specific package versions and their required dependencies are installed. See [collaborating with renv](https://rstudio.github.io/renv/articles/collaborating.html) for instructions on how to restore the project library locally.__
## About the Data
The data was acquired from the University of Florida Integrated Data Repository (IDR) under the aegis of IRB #201902780. The principal investigator on this IRB is James L Wynn, MD. The data sets are exports from the IDR's Epic Clarity system.
## Current Scripts
- [`functions.R`](functions.R): contains the data transformation functions used to create the nsofa components. [algorithm_steps.md](algorithm_steps.md) contains the steps for constructing these functions.
- [`make_nsofa_dataset.R`](make_nsofa_dataset.R): creates a dataset of q1hr nsofa scores and a dataset of the max nsofa score within n days of birth
- [`count_and_categorize_respiratory_devices.R`](count_and_categorize_respiratory_devices.R): created the initial version of `categorized_respiratory_devices.xlsx`. This file is used to categorize respiratory devices as indicating that a child is intubated or _not_ intubated. The version of `categorized_respiratory_devices.xlsx` used in these calculation was reviwed and updated by James Wynn.
## Score Calculation
## Developer Notes
Software developers who would like to make contributions to this repository should read the [Developer Notes](developer_notes.md)