cholera-risk 0.2.1

A Monte Carlo simulation for Cholera risk assessment — quantitative transboundary infection risk analysis with configurable parameters

🦠 Cholera Risk Assessment — Monte Carlo Simulation

A Python package for quantitative risk analysis of transboundary cholera infection risk using stochastic Monte Carlo simulation. All parameters (P1–P6) are fully configurable to support any region or scenario.

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📐 Model Overview

The model computes the compound probability of cholera-related mortality through a chain of six risk factors:

P_final = P1 × P2 × P3 × P4 × P5 × P6

Step	Parameter	Description	Default Distribution
P1	Outbreak Probability	Probability of cholera outbreak in source region	Poisson: 1 − e^(−λt), λ = 2779/(22×12)
P2	Infection Rate	Human cholera infection probability	Beta(1605, 24618)
P3	False Negative (Source)	Missed cases in source region	1 − Uniform(0.549, 0.906)
P4	False Negative (Target)	Missed cases in target region	1 − Uniform(0.884, 0.999)
P5	Exposure Risk	Unsafe water × unsafe sanitation	0.11 × 0.01 = 0.0011
P6	Mortality	Case fatality rate	0.03

Note: All default values above can be overridden. Pass custom P1–P6 values to adapt the model to any region or scenario.

The simulation generates 10,000 (configurable) random samples and computes:

• Expected Probability (mean)
• 90% Confidence Interval (5th–95th percentile)
• Min/Max range
• Sensitivity analysis via Spearman's rank correlation

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📦 Installation

# Install from PyPI
pip install cholera-risk

# Or install a specific version
pip install cholera-risk==0.2.0

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🚀 Quick Start

Using the Class API

from cholera_risk import CholeraSimulator

# Create simulator with 10,000 samples
sim = CholeraSimulator(n_samples=10000, seed=42)

# Run the Monte Carlo simulation
results = sim.run_simulation()

# Access results
print(f"Expected Risk: {results['summary']['expected_prob']:.6e}")
print(f"90% CI: [{results['summary']['ci_5']:.2e}, {results['summary']['ci_95']:.2e}]")

Using the Convenience Function

from cholera_risk.model import quick_risk_assessment

results = quick_risk_assessment(n_samples=50000, seed=123)
print(f"Risk: {results['summary']['expected_prob']:.6e}")

Generating Visualizations

from cholera_risk import CholeraSimulator
from cholera_risk.visualization import plot_all, print_summary

sim = CholeraSimulator(n_samples=10000, seed=42)
results = sim.run_simulation()

# Print formatted summary
print_summary(results)

# Generate all plots (histogram, sensitivity, scatter)
plot_all(results, save_dir="./output_plots/")

Custom P Values (v0.2.0+)

from cholera_risk import CholeraSimulator

# Override specific P values
sim = CholeraSimulator(
    n_samples=10000, seed=42,
    P1=0.95,       # Custom outbreak probability
    P5=0.002,      # Custom exposure risk
    P6=0.05,       # Custom mortality rate
)
results = sim.run_simulation()

# Override ALL P values
sim = CholeraSimulator(
    P1=0.99, P2=0.06, P3=0.27, P4=0.06, P5=0.0011, P6=0.03
)
results = sim.run_simulation()

Advanced: Custom Distribution Parameters

from cholera_risk.model import CholeraSimulator, SimulationConfig

# Customize underlying distributions for a different region
config = SimulationConfig(
    total_outbreaks=3000,
    observation_years=25,
    beta_alpha=2000,
    beta_beta=30000,
    sensitivity_bangladesh_low=0.60,   # Source region sensitivity
    sensitivity_bangladesh_high=0.95,
    sensitivity_india_low=0.80,        # Target region sensitivity
    sensitivity_india_high=0.99,
    unsafe_water_fraction=0.15,
    case_fatality_rate=0.05,
)

sim = CholeraSimulator(n_samples=20000, seed=99, config=config)
results = sim.run_simulation()

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🧪 Running Tests

# Run all tests
python -m pytest tests/ -v

# Run with coverage
python -m pytest tests/ -v --cov=cholera_risk --cov-report=term-missing

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📁 Directory Structure

cholera/
├── cholera_risk/              # The Python package
│   ├── __init__.py            # Package init, exports CholeraSimulator
│   ├── model.py               # Core simulation logic (math & stats)
│   └── visualization.py       # Plotting functions (matplotlib/seaborn)
├── tests/                     # Unit tests (26 tests)
│   ├── __init__.py
│   └── test_model.py
├── README.md                  # This file
├── LICENSE                    # MIT License
├── requirements.txt           # Python dependencies
└── setup.py                   # Package installation script

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📊 Output Example

=================================================================
   CHOLERA RISK ASSESSMENT — Monte Carlo Simulation Results
=================================================================
  Samples:              10,000
  Random Seed:          42
  λ (Poisson rate):     10.5265
-----------------------------------------------------------------
  Expected Probability: 3.207426e-08
  Median:               2.450000e-08
  90% CI:               [3.16e-09, 7.74e-08]
  Minimum:              2.67e-10
  Maximum:              1.05e-07
-----------------------------------------------------------------
  Sensitivity Analysis (Spearman ρ):
    P2 (Infection Rate):  ρ = 0.0397
    P3 (FN Source):       ρ = 0.4899
    P4 (FN Target):       ρ = 0.8312
=================================================================

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🔬 Methodology

• Monte Carlo Simulation: Generates thousands of random scenarios by sampling each stochastic input from its probability distribution
• Beta Distribution (P2): Models the uncertainty in human infection rates using Bayesian parameters derived from epidemiological data
• Uniform Distributions (P3, P4): Represent the range of CholKit RDT diagnostic sensitivity
• Spearman Rank Correlation: Non-parametric measure of how strongly each input drives variations in the output

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📝 License

MIT License — see LICENSE for details.

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👥 Authors

• Navnath Kamble — [e-mail]
• Yamini Madugu — [e-mail]