Reff 0.0.2

effective reproduction number

Reff: effective reproduction number

Reff(data, si_mean, si_sd, tau=7, conf=0.95, mu=5):
input:
  data = daily number of incidence
  si_mean = mean of serial interval
  si_sd = standard deviation of serial interval
  tau = length of time window (integer in days)
  conf = confidence level of estimated Reff
  mu = mean of prior ditribution of Reff
return:
  R = daily Reff of shape (3,len(data))
  R[0:3] = median, min, max
reference:
  A. Cori et al
    American Journal of Epidemiology 178 (2013) 1505
      Web Appendix 1

example code:

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from Reff import Reff

# data from:
# https://github.com/nychealth/coronavirus-data
data = pd.read_csv('case-hosp-death.csv')
t = np.array(pd.to_datetime(data['DATE_OF_INTEREST']))
c = np.array(data['CASE_COUNT'])
R = Reff(c, 6.3, 4.2)
plt.semilogy(t, R.T)
plt.show()