Data science experiments with Johns Hopkins COVID-19 dataset
Jay Urbain, PhD
Last update: 5/10/2020
The spread of a pathogen can start out slowly, but as larger numbers of the susceptible population become infected, the number of infected experiences exponential growth. Eventually this growth levels off as the size of the susceptible population decreases and the populations of the infected and recovered increase.
This can be modeled with variations of logistic (sigmoid) functions.
Data from the reference regions (Italy, South Korea, and Hubei province China) are each fitted with a logistic function beginning on the day of the 100th confirmed case in that country.
The models for the three countries are then scaled to the U.S. population and aligned along the time-axis to best fit the US data for total confirmed cases.
Graphing these projections together demonstrates how the U.S. compares to benchmark regions, to help give more clarity in what the U.S. path going forward might look like.
It is not clear that the US has passed an inflection point, so expect the model to be highly variable.
On the positive side, the percent change in US cases has been steadily decreasing. When this value goes below zero, the number of new cases reported each day will start to decrease.
References:
Interview Ari Libsker, Corona Is Slowing Down, Humanity Will Survive, Says Biophysicist Michael Levitt, 3/13/20. https://www.calcalistech.com/ctech/articles/0,7340,L-3800632,00.html
Chowell, G., Sattenspiel, L., Bansal, S., & Viboud, C. (2016). Mathematical models to characterize early epidemic growth: A review. Physics of life reviews, 18, 66โ97. https://doi.org/10.1016/j.plrev.2016.07.005
2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE https://github.com/CSSEGISandData/COVID-19
Exponential growth and epidemics, CDC https://www.youtube.com/watch?v=Kas0tIxDvrg
Estimating actual COVID 19 cases (novel corona virus infections) in an area based on deaths, CDC https://www.youtube.com/watch?v=mCa0JXEwDEk
Mathematics of the Corona outbreak โ with professor Tom Britton https://www.youtube.com/watch?v=gSqIwXl6IjQ