calc_reproduction_number_wt: Estimate the time dependent reproduction number according to...

In SC-COSMO/sccosmomcma: Stanford-CIDE COronavirus Simulation MOdel (SC-COSMO) for Mexico City Metropolitan Area Analysis

Description

calc_reproduction_number_wt calculates the time-dependent reproduction number according to Wallinga & Teunis.

Usage

calc_reproduction_number_wt(l_out_cosmo, v_time = 2:20, nsim_chosen = 200)

Arguments

l_out_cosmo	List with output from SC-COSMO and all parameters.
v_time	Vector with times at which the time-dependent reproduction number is desired to be calculated.
nsim_chosen	Number of simulations used by the WT algorithm to compute confidence intervals which are often not used. Hence the number is small. The default for WT in the package is 10,000 which uses a very large amount of memory and is not appropriate for parallelization because we will run out of RAM. The default is set to a much smaller number.

Value

A data.frame with with the time-dependent reproduction number.

References

1. Wallinga, J., & Teunis, P. (2004). Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures. American Journal of Epidemiology, 160(6), 509–516. https://doi.org/10.1093/aje/kwh255

SC-COSMO/sccosmomcma documentation built on Dec. 18, 2021, 11:56 a.m.