EpiEstim_wrapper: EpiEstim wrappers arguments

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

EpiEstim wrappers arguments

Description

EpiEstim wrappers arguments

Arguments

minimum_cumul_incidence	Numeric value. Minimum number of cumulated infections before starting the Re estimation. Default is 12 as recommended in Cori et al., 2013.
mean_serial_interval	Numeric positive value. mean_si for estimate_R
std_serial_interval	Numeric positive value. std_si for estimate_R
mean_Re_prior	Numeric positive value. mean prior for estimate_R
output_HPD	Boolean. If TRUE, return the highest posterior density interval with the output.
import_incidence_input	NULL or module input object. List with two elements: A numeric vector named values: the incidence recorded on consecutive time steps. An integer named index_offset: the offset, counted in number of time steps, by which the first value in values is shifted compared to a reference time step This parameter allows one to keep track of the date of the first value in values without needing to carry a date column around. A positive offset means values are delayed in the future compared to the reference values. A negative offset means the opposite. If not NULL, this data represents recorded imported cases. And then incidence_input represents only local cases.

Value

If output_HPD = FALSE, value is a module object (a list of the same kind as incidence_input). The values element of the list then contains the Re estimates. If output_HPD = TRUE, a list of three module objects is returned.

• Re_estimate contains the Re estimates.

• Re_highHPD and Re_lowHPD contain the higher and lower boundaries of the HPD interval, as computed by estimate_R

covid-19-Re/estimateR documentation built on Sept. 14, 2024, 5:49 a.m.