estimate_R_cl_rep: Ensemble estimate of Rt

In ern: Effective Reproduction Number Estimation

Ensemble estimate of Rt

Description

Ensemble estimate of Rt

Usage

estimate_R_cl_rep(
  cl.daily,
  dist.repfrac,
  dist.repdelay,
  dist.incub,
  dist.gi,
  prm.R,
  silent = FALSE,
  RL.max.iter = 10
)

Arguments

cl.daily	Dataframe of inferred daily incidence.
dist.repfrac	List. Parameters for the reporting fraction distribution in the same format as returned by def_dist().
dist.repdelay	List. Parameters for the reporting delay distribution in the same format as returned by def_dist().
dist.incub	List. Parameters for the incubation period distribution in the same format as returned by def_dist().
dist.gi	List. Parameters for the generation interval distribution in the same format as returned by def_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.
silent	Logical. Flag to suppress all output messages, warnings, and progress bars.
RL.max.iter	Integer. Maximum of iterations for the Richardson-Lucy deconvolution algorithm.

Value

A summary of individual Rt realizations with 95% confidence intervals

See Also

EpiEstim::make_config()

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