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[Stable] 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
)

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.

Value

A list summarising the input delay distributions.

See also

convert_to_logmean convert_to_logsd bootstrapped_dist_fit dist_spec

Author

Sebastian Funk

Sam Abbott

Examples

# default settings with a fixed generation time of 1
generation_time_opts()
#> 
#>   Fixed distribution with PMF [0 1]
#> 

# A fixed gamma distributed generation time
generation_time_opts(dist_spec(mean = 3, sd = 2, max = 15))
#> 
#>   Fixed distribution with PMF [0.15 0.13 0.11 0.088 0.076 0.067 0.059 0.053 0.048 0.044 0.041 0.038 0.035 0.033 0.031]
#> 

# An uncertain gamma distributed generation time
generation_time_opts(
 dist_spec(mean = 3, sd = 2, mean_sd = 1, sd_sd = 0.5, max = 15)
)
#> 
#>   Uncertain lognormal distribution with (untruncated) logmean 3 (SD 1) and logSD 2 (SD 0.5)
#> 

# A generation time sourced from the literature
dist <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
generation_time_opts(dist)
#> 
#>   Uncertain gamma distribution with (untruncated) mean 3.6 (SD 0.71) and SD 3.1 (SD 0.77)
#>