Generation Time Distribution Options

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

Usage

generation_time_opts(
  dist = Fixed(1),
  ...,
  disease,
  source,
  max = 14,
  fixed = FALSE,
  tolerance = 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.

...

deprecated; use dist instead

disease

deprecated; use dist instead

source

deprecated; use dist instead

max

deprecated; use dist instead

fixed

deprecated; use dist instead

tolerance

Numeric; the desired tolerance level.

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 <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()
#> Warning: No generation time distribution given. Assuming a fixed generation time of 1 day, i.e. the reproduction number is the same as the daily growth rate. If this was intended then this warning can be silenced by setting `dist` explicitly to `Fixed(1)`.
#> - fixed value:
#>   1

# A fixed gamma distributed generation time
generation_time_opts(Gamma(mean = 3, sd = 2, max = 14))
#> - gamma distribution (max: 14):
#>   shape:
#>     2.2
#>   rate:
#>     0.75

# 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
  )
)
#> Warning: Uncertain gamma distribution specified in terms of parameters that are not the "natural" parameters of the distribution (shape, rate). Converting using a crude and very approximate method that is likely to produce biased results. If possible, it is preferable to specify the distribution directly in terms of the natural parameters.
#> - gamma distribution (max: 14):
#>   shape:
#>     - normal distribution:
#>       mean:
#>         2.2
#>       sd:
#>         0.72
#>   rate:
#>     - normal distribution:
#>       mean:
#>         0.75
#>       sd:
#>         0.41

# An example generation time
generation_time_opts(example_generation_time)
#> - gamma distribution (max: 14):
#>   shape:
#>     - normal distribution:
#>       mean:
#>         1.4
#>       sd:
#>         0.48
#>   rate:
#>     - normal distribution:
#>       mean:
#>         0.38
#>       sd:
#>         0.25