ern (version 2.1.2)

inc2R_one_iter: Helper function. Converts wastewater to Rt after sampling one fecal shedding and one generation interval distribution.

Description

Helper function. Converts wastewater to Rt after sampling one fecal shedding and one generation interval distribution.

Usage

inc2R_one_iter(
  i,
  dist.fec,
  dist.gi,
  ww.conc,
  scaling.factor,
  prm.R,
  silent,
  RL.max.iter
)

Value

List. Elements include inc (incidence) and rt

(reproduction number)

Arguments

i

Numeric. Iteration index. (not used but required when using lapply())

dist.fec

List. Parameters for the fecal shedding 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().

ww.conc

Data frame. Must have variables:

• date: calendar date of wastewater collection

• value: pathogen concentration

scaling.factor

Numeric. Scaling from wastewater concentration to prevalence. This value may be assumed or independently calibrated to data.

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.