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Modelling COVID-19 using SIR-like models

Project description

Epidemia

Epidemia is a Python library that simulates epidemic outbreaks using a SIR-like model.

Install

pip install epidemia

It is recommended to use PyPy instead of CPython (the default Python interpreter) if you have performance problems.

Models

The following SIR-like models have been implemented.

  • SIR: susceptible, infected, recovered model
  • SEIR: susceptible, exposed, infected, recovered model
  • ModelReport2: the model defined in report 2 at COVID-19 en Chile

Optimization methods

List of available optimization methods.

From experience it is necessary to have a good initial estimate of parameters before fitting. An initial optimization round using either annealing or especially PSO work very well. For improved speed it is recommended to use the fast=True flag for naive integration. Finally, an L-BFGS-B with fast=False (i.e. using RK4) will tweak the parameters to fit the curve as best as possible.

Examples

Jupyter notebooks of trained models for specific countries.

Simulating

We need to define the start time and initial state the compartments are in. Using a parameter function we can feed parameter values to the model dependent on time. To run the simulation we additionally define the end time.

import numpy as np

from epidemic import *

# Initial time and state
t0 = np.datetime64('2020-01-01')
y0 = {'S': 1e7, 'E': 200, 'Im': 200, 'I': 20, 'H': 0, 'Hc': 0, 'R': 0, 'D': 0}

# Our alpha at time 't'
def α(t):
    if t >= np.datetime64('2020-06-01') and t < np.datetime64('2020-09-01'):
        return 0.5
    return 1.0

# Our parameters at time 't'
params = lambda Y,t: {
    'βE': α(t) * 0.062015625,
    'βIm': α(t) * 0.12403125,
    'βI': α(t) * 0.165375,
    'βH': α(t) * 0.0,
    'βHc': α(t) * 0.0,
    'γE': 0.2,
    'γIm': 0.1,
    'γI': 0.1,
    'γH': 0.1666,
    'γHc': 0.1,
    'μb': 3.57e-5,
    'μd': 1.57e-5,
    'φEI': 0.50,
    'φIR': 0.85,
    'φHR': 0.85,
    'φD': 0.50,
}

# Create and run model till time 'tmax'
model = ModelReport2()
epidemic = Epidemic(model, t0, tmax=np.datetime64('2021-06-01'))
epidemic.run(y0, params)
epidemic.run_parameter('R_effective', model.R_effective)

epidemic.plot('Epidemic', cols=['I', 'H', 'Hc', 'D'])
epidemic.plot_params('Epidemic (R effective)', cols=['R_effective'])

See example.py.

Example

Training parameters

In order to train our parameters, we define a mapping function x_params: x => params with bounds x_bounds for x. The first parameter to x_params is the initial state y0, and the following parameters are those that are being optimized. The x_params function will return a new initial state y0 and a new params function to define how parameters develop over time (see above).

First we load our model like above, but we pass a data DataFrame from which we can calculate the error. The DataFrame must have column names that correspond to the model's compartments and derived compartments (more on that later). We define our training variables, bounds and function in order to train the model.

# Define our training parameters: initial value, bounds, and mapping function to model parameters
x = [
    0.74,   # E0
    10.3,   # Im0
    0.38,   # CE
    0.75,   # CIm
    0.165,  # βI
    0.2,    # γE
    0.1,    # γIm
    0.1,    # γI
    0.1667, # γH
    0.1,    # γHc
]

x_bounds = [
    (0,20),        # E0
    (0,20),        # Im0
    (0.0,0.4),     # CE
    (0.0,0.9),     # CIm
    (0.0,0.75),    # βI
    (0.17,0.25),   # γE
    (0.07,0.14),   # γIm
    (0.07,0.14),   # γI
    (0.1,0.5),     # γH
    (0.0625,0.14), # γHc
]

def x_params(E0, Im0, CE, CIm, βI, γE, γIm, γI, γH, γHc):
    y0 = {
        'S': 1e7,
        'E': E0 * I0,
        'Im': Im0 * I0,
        'I': I0,
        'H': 0,
        'Hc': 0,
        'R': 0,
        'D': D0,
    }

    λ1 = np.datetime64('2020-04-01')
    κ1 = 0.05
    α2 = 0.75
    α = lambda t: 1.0 if t < λ1 else α2 + (1.0-α2)*np.exp(-κ1*(t-λ1)/np.timedelta64(1,'D'))
    return y0, lambda t: {
        'βE': α(t) * CE * βI,
        'βIm': α(t) * CIm * βI,
        'βI': α(t) * βI,
        'βH': 0.0,
        'βHc': 0.0,
        'γE': γE,
        'γIm': γIm,
        'γI': γI,
        'γH': γH,
        'γHc': γHc,
        'μb': 3.57e-5,
        'μd': 1.57e-5,
        'φEI': 0.5,
        'φIR': 0.6,
        'φHR': 0.6,
        'φD': 0.2,
    }

Now we can train the parameters in x using a variety of methods. Currently implemented are the scipy.optimize.minimize methods, and the scipy.optimize.dual_annealing, scipy.optimize.least_squares, and skopt.*_minimize methods. It is recommended to use fast=True (which doesn't use Runge-Kutta 4 and is this ~4 times faster) for all but the last optimization.

options = {
    'bayesian': {
        'n_calls': 100,
        'n_random_starts': 10,
        'fast': True,
    },
    'annealing': {
        'seed': 1234567,
        'fast': True,
    },
    'L-BFGS-B': {
        'disp': True,
    },
}

for method in ['annealing', 'L-BFGS-B']:
    opt = {}
    if method in options:
        opt = options[method]
    x = epidemic.optimize(x, x_bounds, x_params, method=method, **opt)

epidemic.plot(cols=['I_cases', 'I'])
epidemic.plot(cols=['D'])

See example_train.py.

Example training

Loading data

In order to optimize our simulation, we need to pass training data to the model. The Epidemic class accepts a data argument of that should be a DataFrame, where its columns correspond to the compartments or semi-compartments of the model. For instance, I, or D are valid compartments, but also derived compartments such as the cumulative I_cases or H_cases.

df_infectados = pd.read_csv('data/chile_minsal_infectados.csv', sep=';', index_col=0)
df_infectados = df_infectados.transpose()
df_infectados.index = pd.to_datetime(df_infectados.index, format='%d-%b') + pd.offsets.DateOffset(years=120)

df_fallecidos = pd.read_csv('data/chile_minsal_fallecidos.csv', sep=';', index_col=0)
df_fallecidos = df_fallecidos.transpose()
df_fallecidos.index = pd.to_datetime(df_fallecidos.index, format='%d-%b') + pd.offsets.DateOffset(years=120)

data = pd.DataFrame({
    'I_cases': df_infectados['Región Metropolitana'],
    'D': df_fallecidos['Región Metropolitana'],
})

epidemic = Epidemic(model, t0, tmax, data=data)

Change simulation time range

Given an Epidemic, we can extend the simulation time range. This will run all simulations for the new time range.

epidemic.extend(np.datetime64('2021-06-01'))

Add confidence intervals

When calling run on an Epidemic, we can pass the tag argument. If this is anything but None, empty, or mean, we will assume this is an extra curve that will be saved. If the tag name is lower or upper, it will serve as the lower and upper bounds respectively for the confidence intervals while plotting.

epidemic.run(y0_lower, params_lower, tag='lower')
epidemic.run(y0_upper, params_upper, tag='upper')

# or
epidemic.run(*x_params(*x_lower), tag='lower')
epidemic.run(*x_params(*x_upper), tag='upper')

Visualization and parameter analysis

Plotting data columns

epidemic.plot(cols=['I', 'H', 'Hc', 'D'])

Example

Plotting derived parameters

epidemic.plot_params(cols=['Reff'])

Example parameters

Printing parameters

Display the model parameters and their values.

epidemic.print_params()
ParameterValue
βE0.02293
βIm0.06112
βI0.1891
βH0
βHc0
γE0.186
γIm0.1376
γI0.1116
γH0.14
γHc0.0626
μb3.57e-05
μd1.57e-05
φEI0.5
φIR0.6006
φHR0.6049
φD0.2

Printing training parameters

Display the training parameters and their values and ranges.

epidemic.print_x_params(x, x_bounds, x_params)
ParameterValueRange
E00.8514[0, 20]
Im02.526[0, 20]
CE0.1213[0, 0.4]
CIm0.3233[0, 0.9]
βI0.2521[0, 0.75]
γE0.186[0.17, 0.25]
γIm0.1376[0.07, 0.14]
γI0.1116[0.07, 0.14]
γH0.14[0.07, 0.14]
γHc0.0626[0.0625, 0.14]

Printing statistics

Print relevant statistics about the simulation.

epidemic.print_stats()
ParameterValueDate
R effective1.762020-03-15
R effective1.412020-05-01
Fatality0.022020-05-01
max(I)30112020-05-01
max(H)19742020-05-01
max(Hc)11392020-05-01
max(D)1732020-05-01

Parameter sensitivity

Probing parameter sensitivity to the error. Each parameter is moved a small distance epsilon and evaluated to see how much it impacts the error. Higher values means these parameter are very sensitive. When zero it means it has no impact on the error and is thus independent.

Each column shows the impact of the error on that data series, while * is the total model error.

epidemic.param_sensitivity()
* D I_cases
E0 0.0025952 0.00267847 0.00253102
Im0 0.000353852 0.000319161 0.00036079
CE 0.00634905 0.00140165 0.0113138
CIm 0.00543327 0.00270623 0.00813083
βI 0.0271594 0.00895137 0.0453727
γE 0.0110189 0.0161675 0.00588935
γIm 0.0115601 0.00123512 0.0219025
γI 0.00850704 0.0615199 0.0445023
γH 0.0087152 0.0174582 0
γHc 0.00790336 0.0157928 0

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