EpiEstim wrappers arguments

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:

  1. A numeric vector named values: the incidence recorded on consecutive time steps.

  2. 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