README.md

CovidDataHandler

This project contains a variety of methods to help fetch and transform data pertaining to COVID from the CDC.

Everything in this repository was made to prepare data for Sum COVID.

Up and Running

Project Dependencies

First, install Elixir. Next, install the project dependencies with:

mix deps.get

Configuring API Keys and Output

Copy .example.env as .env and complete the environment variables as needed.

You'll need an app key from the CDC API to fetch data. You can register for a Socrata account here. You'll then need to create an app token. The same app token can be used on different datasets.

Module Explanation and Use

Modules

All functions are broken out into modules based on the CDC `dataset they work with. Currently:

• CaseSurveillance handles the "COVID-19 Case Surveillance Public Use Data" from the CDC's API
• DataTracker handles data downloaded from the COVID Data Tracker
• DeathsByCause handles the "Monthly Provisional Counts of Deaths by Select Causes, 2020-2021" from the CDC's API
• Flu handles data downloaded from "Pneumonia, Influenza, and COVID-19 Mortality from the National Center for Health Statistics Mortality Surveillance System"
• Vaers handles data exported from the CDC's WONDER VAERS data

Use

First, from your terminal:

source .env
iex -S mix

COVID-19 Case Surveillance Public Use Data

First, register an app token with the CDC Socrata API.

To get combined cases and deaths by age:

CaseSurveillance.save_cases_by_age_data()
CaseSurveillance.save_deaths_by_age_data()
CaseSurveillance.get_combined_age_output()

To get deaths by underlying medical condition classification:

CaseSurveillance.save_deaths_by_medcond()

COVID Data Tracker

First, download the daily case and death table data from the CDC. To transform the CSV to JSON:

DataTracker.get_daily_deaths_output()
DataTracker.get_daily_cases_output()
DataTracker.get_seven_day_moving_average_cfr_output()

Pneumonia, Influenza, and COVID-19 Mortality from the National Center for Health Statistics Mortality Surveillance System

First, download the chart data from the CDC. To transform the CSV to JSON:

Flu.get_weekly_flu_output()

Monthly Provisional Counts of Deaths by Select Causes, 2020-2021

First, register an app token with the CDC Socrata API.

To get the monthly deaths by cause:

DeathsByCause.save_monthly_deaths_by_cause_2020_2021()

To calculate the deaths by cause for the year of 2020:

DeathsByCause.save_monthly_deaths_by_cause_2020_2021()
DeathsByCause.get_2020_causes_of_death()

VAERS Data

First, export the text file of the VAERs data from the CDC WONDER system. Ensure that "Show Totals" is not selected. To transform to JSON, manually delete the footer from the text file, then run:

Vaers.get_all_vaccine_events_by_year()