# Reproducing Riou & Althaus (2020)¶

## Approximate Bayesian Computation¶

In this short tutorial, we’ll show you how to reproduce the results of Riou & Althaus (2020), which showed that the early COVID-19 in Wuhan, China has $$\mathcal{R}_0 \sim 2$$ using Approximate Bayesian Computation.

First we’ll import some of the required packages and eugene:

import numpy as np
import matplotlib.pyplot as plt
from glob import glob

from eugene import abc


Next we’ll set the parameters of the run, which we explain below:

params = dict(
# Grid of R0 and k parameters to iterate over
R0_grid = np.logspace(np.log10(0.7), np.log10(10), 50),
k_grid = np.logspace(-2, 1, 10),

# Maximum number of cases to run the simulation through (should be
# greater than max_number_cases)
max_cases = 1e4,

# Maximum number of days someone might transmit the disease
max_time = 90,   # days

# Number of stochastic trials to run at each grid-point
trials = 1000,

# Days elapsed since zoonotic transmission
days_elapsed_min = [46-7, 52-7],  # days
days_elapsed_max = [46+7, 52+7],  # days

# Number of cases after days_elapsed
min_number_cases = [190, 1000],  # cases
max_number_cases = [5590, 9700],  # cases

# Initial number of index cases n (day-zero cases)
n_min = 1,   # cases
n_max = 100,  # cases

# Generation interval/Gamma function shape parameter
gamma_shape_min = 1,
gamma_shape_max = 5,

# Generation time interval D
D_min = 7,   # days
D_max = 60,  # days

# Computer parameters
n_processes = 16,
n_grid_points_per_process = 2,

# Formatting string for naming simulation outputs
samples_path = 'samples/samples{0}.npy'
)


The number of processes n_processes should be equivalent to the number of processes you can run simultaneously on your machine. n_grid_points_per_process determines the number of $$\mathcal{R}_0$$ grid points distributed to each process. The samples_path argument will determine where to put the chains from the rejection sampler – you’ll need to create a samples/ directory for this example to work.

Finally, we can run the simulation with the following:

total_trials = (params['trials'] * params['R0_grid'].shape[0] *
params['k_grid'].shape[0])
print(f'Total number of simulations triggered: {total_trials}')

abc(**params)


The Approximate Bayesian Computation abc function will run simple parallel processes that each save the accepted chains from a rejection sampler algorithm.

## Visualizing the results¶

We can view the acceptance rate of the chains as a function of $$\mathcal{R}_0$$ and $$k$$ with the following commands:

R0_grid = params['R0_grid']
k_grid = params['k_grid']
trials = params['trials']

samples = np.vstack([np.load(p) for p in glob('samples/samples*.npy')])

lo, mid, hi = np.percentile(samples[:, 0], [16, 50, 84])
print(f'R0 = {mid:.2f}_{{-{mid-lo:.2f}}}^{{+{hi-mid:.2f}}}')

hist2d, xedges, yedges = np.histogram2d(np.log10(samples[:, 0]),
np.log10(samples[:, 1]),
bins=[R0_grid.shape[0],
k_grid.shape[0]])

fig, ax = plt.subplots(figsize=(5, 4))

X, Y = np.meshgrid(R0_grid, k_grid)

im = ax.pcolor(Y, X, hist2d.T / trials, cmap=plt.cm.Reds)

ax.set_xscale('log')
ax.set_yscale('log')

cbar = plt.colorbar(im, label='Acceptance fraction')

ax.set(xlabel='$k$', ylabel='$\mathcal{R}_0$')
fig.savefig('plots/grid.pdf', bbox_inches='tight')
plt.show()


The plot above shows the acceptance rate of the ABC rejection sampler as a function of $$\mathcal{R}_0$$ and $$k$$, darker red represents higher acceptance rates, meaning a better match between the simulated cumulative incidence curves and the observations. The median $$\mathcal{R}_0 \sim 2$$, meaning for every case of COVID-19 there are approximately two new cases generated, and $$k \gtrsim 0.1$$.

## Parameter degeneracies¶

Since we sampled for a range of $$\mathcal{R}_0, k, D, n$$, and gamma_shape parameters which we will call $$\alpha$$, we can plot the fraction of accepted rejection sampler iterations as a function of each combination of these parameters to examine how the uncertainty on one parameter propagates into uncertainties on the others.

We can generate a corner plot with our results like so:

from corner import corner

key_text = """Key:

$\log \mathcal{R}_0$: Reproduction number
$\log k$: Dispersion factor
$D$: Generation time interval [days]
$n$: Number of index cases
$\Delta t$: Time since index case [days]
$\\alpha$: Gamma function shape parameter"""

std_bin_size = 25
bins = [std_bin_size, std_bin_size - 15, std_bin_size, std_bin_size - 5,
std_bin_size, std_bin_size]

samples[:, 0] = np.log10(samples[:, 0])
samples[:, 1] = np.log10(samples[:, 1])

hist_kwargs = dict(plot_contours=False, plot_datapoints=False,
no_fill_contours=False, bins=bins)

corner(samples, labels=['$\log \mathcal{R}_0$', '$\log k$', '$D$', '$n$',
'$\Delta t$', '$\\alpha$'],
smooth=True, contour=False, **hist_kwargs)

plt.annotate(key_text, xy=(0.55, 0.8), fontsize=18,
ha='left', va='bottom', xycoords='figure fraction')

plt.savefig('plots/corner.pdf', bbox_inches='tight')
plt.show()


We investigate the larger uncertainties and long tail towards large $$\mathcal{R}_0$$ with the “corner plot” above. The diagonal elements in the matrix of plots (histograms) represent the posterior distributions for each parameter (see label for each column in the bottom row). The off-diagonal elements represent joint posterior distributions for each pair of model parameters, and darker pixels represent a higher density of posterior samples. Note for example that the 2D histogram in the second row, first column is the same as the figure above (with its axes swapped). The corner plot is useful for examining degeneracies between parameters, which are visible as correlations between model parameters.

There are degeneracies between four pairs of model parameters. First, simulated epidemics can reproduce the observed cumulative incidence on 18 Jan 2020 equally well with small $$\mathcal{R}_0$$ and small $$D$$, or with larger $$\mathcal{R}_0$$ and larger $$D$$. There is degeneracy between $$\mathcal{R}_0$$ and the $$\Gamma$$-function shape parameter $$\alpha$$ the observed cumulative incidence is reproduced equally well with $$\log_{10}\mathcal{R}_0 = 0.2$$ and $$\alpha=5$$, or with $$\log_{10}\mathcal{R}_0 = 1$$ and $$\alpha=1$$. There are also degeneracies between $$\mathcal{R}_0$$ and $$n$$, and $$\alpha$$ and $$D$$.