Metadata-Version: 2.1
Name: Reff
Version: 0.0.2
Summary: effective reproduction number
Home-page: https://github.com/tt-nakamura/Reff
Author: Takahiro Nakamura
Author-email: a41757@gmail.com
License: UNKNOWN
Description: # 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()
        ```
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
