compute_t_min: Compute the smallest index at which joint estimation should...

In annecori/EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Compute the smallest index at which joint estimation should start

Description

Unless specified by the user, t_min in estimate_advantage is computed as the sum of two indices: (i) the first day of non-zero incidence across all locations, computed using first_nonzero_incid and (ii) the 95th percentile of the probability mass function of the SI distribution across all variants computed using compute_si_cutoff

Usage

compute_t_min(incid, si_distr, miss_at_most)

Arguments

incid	a multidimensional array containing values of the incidence for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension)
si_distr	a matrix with two columns, each containing the probability mass function for the discrete serial interval for each of the two pathogen/strain/variants, starting with the probability mass function for day 0 in the first row, which should be 0. each column in the matrix should sum to 1
miss_at_most	numeric. probability mass in the tail of the SI distribution

Value

integer

Author(s)

Sangeeta Bhatia

annecori/EpiEstim documentation built on Sept. 7, 2024, 7:34 p.m.