incidence_to_R: Estimate Rt using EpiEstim

In ern: Effective Reproduction Number Estimation

Estimate Rt using EpiEstim

Description

Estimate Rt using EpiEstim

Usage

incidence_to_R(incidence, generation.interval, prm.R)

Arguments

incidence	Data frame. Estimated incidence. Must include at least date, I, and t columns.
generation.interval	List. Parameters for a single generation interval distribution, as generated by sample_a_dist().
prm.R	List. Settings for the ensemble when calculating Rt. Elements include: iter: Integer. Number of iterations for the Rt ensemble CI: Numeric between 0 and 1. Confidence interval width for Rt estimates after sampling uncertain distributions. window: Integer. Number of days defining the window of data used by EpiEstim to estimate Rt. If NULL, will default to 7. config.EpiEstim: (optional) configuration for EpiEstim defined via EpiEstim::make_config(). If NULL, will use default config from EpiEstim.

See Also

def_dist()

EpiEstim::make_config()

ern documentation built on April 4, 2025, 2:13 a.m.