Delay Distribution Options

Returns delay distributions formatted for usage by downstream functions.

Usage

delay_opts(
  dist = Fixed(0),
  default_cdf_max = getOption("EpiNow2.cdf_max", 0.999),
  weight_prior = TRUE,
  default_cdf_cutoff = lifecycle::deprecated()
)

Arguments

dist

A delay distribution or series of delay distributions. Default is a fixed distribution with all mass at 0, i.e. no delay.

default_cdf_max

Numeric; default CDF level to keep the distribution up to if an unconstrained distribution is passed as dist. If dist is already constrained by having a maximum or CDF level this is ignored. Note that this can only be done for <dist_spec> objects with fixed parameters. Defaults to getOption("EpiNow2.cdf_max", 0.999), so a session-wide default can be set with, e.g., options(EpiNow2.cdf_max = 0.995).

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.

default_cdf_cutoff

Use default_cdf_max instead.

Value

A <delay_opts> object summarising the input delay distributions.

See also

distspec::convert_to_logmean() distspec::convert_to_logsd() bootstrapped_dist_fit() distspec::Distributions vignette("delays") for background on delay distributions

Examples

# no delays
delay_opts()
#> - fixed value:
#>   0

# A single delay that has uncertainty
delay <- LogNormal(
  meanlog = Normal(1, 0.2),
  sdlog = Normal(0.5, 0.1),
  max = 14
)
delay_opts(delay)
#> - lognormal distribution (max: 14):
#>   meanlog:
#>     - normal distribution:
#>       mean:
#>         1
#>       sd:
#>         0.2
#>   sdlog:
#>     - normal distribution:
#>       mean:
#>         0.5
#>       sd:
#>         0.1

# A single delay without uncertainty
delay <- LogNormal(meanlog = 1, sdlog = 0.5, max = 14)
delay_opts(delay)
#> - lognormal distribution (max: 14):
#>   meanlog:
#>     1
#>   sdlog:
#>     0.5

# Multiple delays (in this case twice the same)
delay_opts(delay + delay)
#> Composite distribution:
#> - lognormal distribution (max: 14):
#>   meanlog:
#>     1
#>   sdlog:
#>     0.5
#> - lognormal distribution (max: 14):
#>   meanlog:
#>     1
#>   sdlog:
#>     0.5