Generation Time Distribution Options

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.

Value

A <generation_time_opts> object summarising the input delay distributions.

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.

Examples

# default settings with a fixed generation time of 1
generation_time_opts()
#> Warning: ! No generation time distribution given.
#> ℹ Now using a fixed generation time of 1 day, i.e. the reproduction number is
#>   the same as the daily growth rate.
#> ℹ If this was intended then this warning can be silenced by setting `dist =
#>   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 and rate.
#> ℹ Converting using a crude and very approximate method that is likely to
#>   produce biased results.
#> ℹ 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
gt_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