COVID-19-Hospitalization-Trends

This repository contains the code used to analyze United States National and Regional COVID-19 hospitalization trends in both children and adult populations.

View Completed Analysis, Stats, and Figures

In Progress:

View Our Interactive Dashboard using Hospital Level Data

About the Data

The analysis examines COVID-19 Hospitalizations as reported weekly from all 50 states including the District of Columbia, from July 31, 2020 until April 15, 2021.

Data was acquired through the United States Department of Health and Human Services (HHS)[1,2]

Helpful FAQ Resource[3]

Hospitalization rates were standardized per 100,000 adults or children using the U.S Census Bureau's 2020 National and Regional population estimates[4]

Vaccination data was aquired from the CDC[5]

To Run Notebook

1. Clone this repo:

git clone https://github.com/meghutch/COVID-19-Hospitalization-Trends.git

2. Run Hospitalizations_Trends.Rmd

3. (Optional): Download latest data from the (HHS) and replace the new file name:

hhs_data <- read_csv('data/new_file_name_here.csv)

Optional Analyses to Explore Include:

Hospitalizations_Trends_Hospital_Level.Rmd: Explore hospitalization trends with Hospital level data[6]
Hospitalization_Trends_Vacciniation.Rmd: Explore preliminary vaccinination trends

Analysis

The Analysis reports the median standardized hospitalization rates and plots figures of the trends. The change point analysis finds identifies the most likely time point for an upward shift in mean hospitalizations [7] (R/change_point_function.R written by Molei Liu)

References

COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries. HealthData Web site. Updated April 17, 2021. Accessed April 22, 2021. https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/g62h-syeh https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/g62h-syeh
COVID-19 Guidance for Hospital Reporting and FAQs. Human and Health Services Web site. U.S. Department of Human and Health Services. Updated March 19, 2021. Accessed March 25, 2020. https://www.hhs.gov/sites/default/files/covid-19-faqs-hospitals-hospital-laboratory-acute-care-facility-data-reporting.pdf
Facility COVID PUF Community FAQ. Github Web site. Updated December 15, 2020. Accessed February 24, 2021. https://github.com/CareSet/COVID_Hospital_PUF?src=hd
SC-EST2020-18+POP-RES. U.S. Census Bureau, Population Division. 2020. Accessed February 9, 2020. https://www2.census.gov/programs-surveys/popest/datasets/2010-2020/national/totals/
Demographic Trends of People Receiving COVID-19 Vaccinations in the United States. Center for Disease Control and Prevention. Updated June 11, 2021. Accessed June 11, 2021. https://covid.cdc.gov/covid-data-tracker/#vaccination-demographics-trend
COVID-19 Reported Patient Impact and Hospital Capacity by Facility. HealthData Web site. Updated March 29, 2021. Accessed March 29, 2021. https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/anag-cw7u
Zhang, N. R., Siegmund, D. O., Ji, H., and Li, J. Z. Detecting simultaneous changepoints in multiple sequences. Biometrika. 2010;97(3):631–645.

Data is publicly available under the Public Domain U.S. Government license[1]

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