Cummulative SARS-CoV-2 case counts aggregated at world bank region, country, state, US country levels and cruises.

Biothings parser for COVID-19 case counts and testing rates. Daily reports have been corrected in a fork here that is maintained.

Running

preprocess.py aggregates case count and testing data from multiple sources using shapefiles to standardize the data with iso3 and fips codes. A config.ini is required to run the script with paths to each of the data sources. An example of the config.ini file is given at example.config.ini. This script will take daily report files from JHU CSSE COVID-19 data and aggregate daily cummulative casecounts at world bank region, country, state, US country levels and cruises (Grand Princess and Diamond Princess). It aggregates NYT COVID-19 data to get counts for the US at state and county levels. It adds testing results for US states from covid tracking.

Create a new virtual environment and install the requirements for running the preprocess script with pip install -r requirements.txt. GDAL is also required. Building from source is suggested in preference of using Homebrew, although Linux and Windows users may find their package manager capable of installing without issue.

Data Sources

Shapefiles:

1. Natural Earth: ne_10m_admin_0_countries
2. Natural Earth: ne_10m_admin_1_states_provinces
3. 2019 US County Shapefiles: tl_2019_us_county
4. US Census 2018 CBSA Shapefile

Data:

1. Country GDP per capita
2. US Census Sep 2018 metropolitan CBSA exported as census_metropolitan_areas.csv

Repos

1. JHU CSSE COVID-19 data. A fork of this data with small corrections is available here.
2. NYT US State and County data