delay_opts: Delay Distribution Options

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

Delay Distribution Options

Description

Returns delay distributions formatted for usage by downstream functions.

Usage

delay_opts(dist = Fixed(0), default_cdf_cutoff = 0.001, weight_prior = TRUE)

Arguments

dist	A delay distribution or series of delay distributions. Default is a fixed distribution with all mass at 0, i.e. no delay.
default_cdf_cutoff	Numeric; default CDF cutoff to be used if an unconstrained distribution is passed as dist. If dist is already constrained by having a maximum or CDF cutoff this is ignored. Note that this can only be done for <dist_spec> objects with fixed parameters.
weight_prior	Logical; if TRUE (default), any priors given in dist will be weighted by the number of observation data points, in doing so approximately placing an independent prior at each time step and usually preventing the posteriors from shifting. If FALSE, no weight will be applied, i.e. any parameters in dist will be treated as a single parameters.

Value

A ⁠<delay_opts>⁠ object summarising the input delay distributions.

See Also

convert_to_logmean() convert_to_logsd() bootstrapped_dist_fit() Distributions

Examples

# no delays
delay_opts()

# A single delay that has uncertainty
delay <- LogNormal(
  meanlog = Normal(1, 0.2),
  sdlog = Normal(0.5, 0.1),
  max = 14
)
delay_opts(delay)

# A single delay without uncertainty
delay <- LogNormal(meanlog = 1, sdlog = 0.5, max = 14)
delay_opts(delay)

# Multiple delays (in this case twice the same)
delay_opts(delay + delay)

EpiNow2 documentation built on April 3, 2025, 8:03 p.m.