A tool to estimate Instantaneous Reproduction Number(Rt) for the pandemic
A tool to estimate Instantaneous Reproduction Number(Rt)
cal_r() provide real-time estimation of time-varying distribution of Rt and infected numbers from a range of epidemic observations (e.g., number of onsets and confirmed cases).
dart = DARt(GT,D_s,Filename)
GT: generation time distribution; GT represents the probability that the secondary infection case occurs 1 day after the primary infection.
D_s: delay time distribution; D_s represents the probability that an individual infected is observed after 1 day.
Filename: input file; this file should contain date and corresponding observations, the date should be sorted from the oldest to the latest. See 'Example_input.csv'.
This tool is described in the following paper:'Revealing the Transmission Dynamics of COVID-19: A Bayesian Framework for R_t Estimation'
GT = [0, 0, 0.165720874545241, 0.226350757019051, 0.245007574714227, 0.213515210247327, 0.149405583474155] # 1:7; non-zero index 3:7 D_s = np.array([0, 0, 0, 0, 0, 0, 0.0996906, 0.1130266, 0.1143032, 0.1069238, 0.0937167999999999]) dart = DARt(GT=GT, D_s=D_s, filename='Example_input.csv') dart.cal_r()
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