estimate_R_cl_single: A single realization of the Rt estimate

Description

A single realization of the Rt estimate

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

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.