Epidemic Modeling for Everyone

Repository to accompany the blog series: Epidemic Modeling

These blog posts were recently featured in the Data Exchange Podcast by Ben Lorica in two episodes:

• Computational Models and Simulations of Epidemic Infectious Diseases

• Assessing Models and Simulations of Epidemic Infectious Diseases

Background Information

1. CoVID-19: Everything you need to know

2. CoVID-19: The first truly global event

Visualization

1. Epidemiology001.ipynb - Visualizing the spread of CoVID-19

2. Epidemiology002.ipynb - Visualizing individual CoVID-19 patient data

3. Epidemiology003.ipynb - CoVID-19: Forecasting the death toll

Compartmental Models

1. Epidemiology101.ipynb - Epidemic Modeling 101: Or why your CoVID19 exponential fits are wrong

2. Epidemiology102.ipynb - Epidemic Modeling 102: All CoVID-19 models are wrong, but some are useful

3. Epidemiology103.ipynb - Epidemic Modeling 103: Adding confidence intervals and stochastic effects to your CoVID-19 Models

4. Epidemiology104.ipynb - Epidemic Modeling 104: Impact of Seasonal effects on CoVID-19

5. Epidemiology105.ipynb - Epidemic Modeling 105: Competing CoVID-19 Strains

Network models

1. Epidemiology 201.ipynb - Epidemiology 201: Network Structure, Super-spreaders and Contact Tracing\

2. Epidemiology 202.ipynb - Epidemiology 202: Network Models, the effect of degree correlations

Vaccination

1. Epidemiology 301.ipynb - Epidemiology 301: How to model the effects of vaccination

Resources

• Jupyter notebook includes all the code used to generate the figures in the blog posts. Run the code online using

• EpiModel.py - Python module encapsulates all the code necessary to numerically implement arbitrary compartmental epidemic models

• NetworkEpiModel.py - Python module encapsulates all the code necessary to numerically implement arbitrary epidemic models on networks

Be kept put to date on all things Machine Learning and Data Science right in your mail box. Sign up to The Sunday Briefing newsletter: https://data4sci.com/newsletter