dot-estimate_Re_EpiEstim_piecewise_constant: Estimate Re with EpiEstim in a piecewise-constant fashion

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

Estimate Re with EpiEstim in a piecewise-constant fashion

Description

This function returns piecewise-constant Re estimates.

Usage

.estimate_Re_EpiEstim_piecewise_constant(
  incidence_input,
  import_incidence_input = NULL,
  minimum_cumul_incidence = 12,
  interval_ends = NULL,
  interval_length = 7,
  mean_serial_interval = 4.8,
  std_serial_interval = 2.3,
  mean_Re_prior = 1,
  output_HPD = FALSE
)

Arguments

incidence_input	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.
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.
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.
interval_ends	Use with estimation_method = "EpiEstim piecewise constant" Integer vector. Optional argument. If provided, interval_ends overrides the interval_length argument. Each element of interval_ends specifies the right boundary of an interval over which Re is assumed to be constant for the calculation. Values in interval_ends must be integer values corresponding with the same numbering of time steps as given by incidence_input. In other words, interval_ends and incidence_input, use the same time step as the zero-th time step.
interval_length	Use with estimation_method = "EpiEstim piecewise constant" Positive integer value. Re is assumed constant over steps of size interval_length.
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.

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.