generation_time_opts: Generation Time Distribution Options

Description

Returns generation time parameters in a format for lower level model use. The generation time can either be given as a disease and source to be passed to get_generation_time, or as parameters of a distribution to be passed to dist_spec.

Usage

generation_time_opts(
  dist = dist_spec(mean = 1),
  ...,
  disease,
  source,
  max = 15L,
  fixed = FALSE,
  prior_weight
)

Value

A list summarising the input delay distributions.

Arguments

dist: A delay distribution or series of delay distributions generated using dist_spec() or get_generation_time(). If no distribution is given a fixed generation time of 1 will be assumed.
...: deprecated; use dist instead
disease: deprecated; use dist instead
source: deprecated; use dist instead
max: deprecated; use dist instead
fixed: deprecated; use dist instead
prior_weight: deprecated; prior weights are now specified as a model option. Use the weigh_delay_priors argument of estimate_infections instead.

Author

Sebastian Funk

Sam Abbott

Examples

Run this code

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

# A fixed gamma distributed generation time
generation_time_opts(dist_spec(mean = 3, sd = 2, max = 15))

# An uncertain gamma distributed generation time
generation_time_opts(
 dist_spec(mean = 3, sd = 2, mean_sd = 1, sd_sd = 0.5, max = 15)
)

# A generation time sourced from the literature
dist <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
generation_time_opts(dist)