Covid-19 Simulation (Python)

Simulates the spread of COVID-19 using a per-country sampled population and a simple Markov-chain per-person model.
This assignment-style project creates a per-person daily time-series, a per-country daily summary, and a visualization of infection waves. It also includes a small Streamlit app to run and visualize the results.

Snapshot

• Status: working (no automated CI or packaging yet).
• Language: Python
• Key files: assignment2.py, app.py (Streamlit UI), helper.py, sim_parameters.py, a2-countries.csv, test.py.
• Outputs:
  • a2-covid-simulated-timeseries.csv
  • a2-covid-summary-timeseries.csv
  • a2-covid-simulation.png.

What it does

• Builds sampled populations for selected countries (sample ratio, e.g. 1e6).
• Runs a per-person, daily Markov chain using age-group specific transition probabilities (from sim_parameters.py) between states:
  • H (healthy)
  • I (infected, no symptoms)
  • S (symptomatic)
  • M (immune)
  • D (deceased).
• Saves:
  • a2-covid-simulated-timeseries.csv — long table of person/day/state.
  • a2-covid-summary-timeseries.csv — aggregated counts per country/day for states D, H, I, M, S.
  • a2-covid-simulation.png — chart created by helper.py::create_plot().

Quick setup (local)

1. Create venv and install:

python -m venv .venv
source .venv/bin/activate    # or .venv\Scripts\activate on Windows
pip install --upgrade pip
pip install -r requirements.txt  # or: pip install pandas matplotlib streamlit

2. Run the simulation (default inputs are read from test.py):

# Run assignment script directly (example arguments)
python assignment2.py
# or if the file exposes run() and test.py calls it, run the test driver:
python test.py

3. Run the Streamlit app (interactive):

streamlit run app.py
# then open http://localhost:8501

File Overview

• assignment2.py — main simulator (implements run(countries_csv_name, countries, start_date, end_date, sample_ratio)).
• sim_parameters.py — transition probabilities and holding times per age group.
• helper.py — plotting helper (provides create_plot() used to produce PNG).
• app.py — Streamlit UI that calls assignment2.run(...).
• test.py — example driver and test harness.
• a2-countries.csv — country demographics input.
• ass2.ipynb — notebook used for experimentation.

Outputs (generated by running):

• a2-covid-simulated-timeseries.csv
• a2-covid-summary-timeseries.csv
• a2-covid-simulation.png

Example usage

Run the sim for ["Afghanistan", "Sweden", "Japan"] from 2021-04-01 to 2022-04-30 with sample ratio 1e6. Output CSV + PNG will be written to the project root.

Example Plot Image