generation_time_opts: Generation Time Distribution Options

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

Generation Time Distribution Options

Description

Returns generation time parameters in a format for lower level model use.

Usage

gt_opts(
  dist = Fixed(1),
  ...,
  disease,
  source,
  max = 14,
  fixed = FALSE,
  default_cdf_cutoff = 0.001,
  weight_prior = TRUE
)

generation_time_opts(
  dist = Fixed(1),
  ...,
  disease,
  source,
  max = 14,
  fixed = FALSE,
  default_cdf_cutoff = 0.001,
  weight_prior = TRUE
)

Arguments

dist	A delay distribution or series of delay distributions . If no distribution is given a fixed generation time of 1 will be assumed. If passing a nonparametric distribution the first element should be zero (see Details section)
...	deprecated; use dist instead
disease	deprecated; use dist instead
source	deprecated; use dist instead
max	deprecated; use dist instead
fixed	deprecated; use dist instead
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.
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.

Details

Because the discretised renewal equation used in the package does not support zero generation times, any distribution specified here will be left-truncated at one, i.e. the first element of the nonparametric or discretised probability distribution used for the generation time is set to zero and the resulting distribution renormalised.

Value

A ⁠<generation_time_opts>⁠ object summarising the input delay distributions.

See Also

convert_to_logmean() convert_to_logsd() bootstrapped_dist_fit() Gamma() LogNormal() Fixed()

Examples

# default settings with a fixed generation time of 1
generation_time_opts()

# A fixed gamma distributed generation time
generation_time_opts(Gamma(mean = 3, sd = 2, max = 14))

# An uncertain gamma distributed generation time
generation_time_opts(
  Gamma(
    mean = Normal(mean = 3, sd = 1),
    sd = Normal(mean = 2, sd = 0.5),
    max = 14
  )
)

# An example generation time
gt_opts(example_generation_time)

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