backcalc_opts: Back Calculation Options

In EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Back Calculation Options

Description

Defines a list specifying the optional arguments for the back calculation of cases. Only used if rt = NULL.

Usage

backcalc_opts(
  prior = c("reports", "none", "infections"),
  prior_window = 14,
  rt_window = 1
)

Arguments

prior	A character string defaulting to "reports". Defines the prior to use when deconvolving. Currently implemented options are to use smoothed mean delay shifted reported cases ("reports"), to use the estimated infections from the previous time step seeded for the first time step using mean shifted reported cases ("infections"), or no prior ("none"). Using no prior will result in poor real time performance. No prior and using infections are only supported when a Gaussian process is present . If observed data is not reliable then it a sensible first step is to explore increasing the prior_window wit a sensible second step being to no longer use reported cases as a prior (i.e set prior = "none").
prior_window	Integer, defaults to 14 days. The mean centred smoothing window to apply to mean shifted reports (used as a prior during back calculation). 7 days is minimum recommended settings as this smooths day of the week effects but depending on the quality of the data and the amount of information users wish to use as a prior (higher values equalling a less informative prior).
rt_window	Integer, defaults to 1. The size of the centred rolling average to use when estimating Rt. This must be odd so that the central estimate is included.

Value

A ⁠<backcalc_opts>⁠ object of back calculation settings.

Examples

# default settings
backcalc_opts()

EpiNow2 documentation built on Oct. 31, 2024, 5:09 p.m.