Define epidist family

This function is used within epidist() to create a model specific custom brms family object. This custom family is passed to brms. It is unlikely that as a user you will need this function, but we export it nonetheless to be transparent about what happens inside of a call to epidist().

Usage

epidist_family(data, family = lognormal(), ...)

Arguments

data

An object with class corresponding to an implemented model.

family

A description of the response distribution and link function to be used in the model. Every family function has a link argument allowing users to specify the link function to be applied on the response variable. If not specified, default links are used. For details of all supported families see brms::brmsfamily(). Commonly used, such as brms::lognormal(), are also reexported as part of epidist.

...

Additional arguments passed to fn method.

Value

A brms custom family object.

Details

The family may be any brms family of a positive response, such as brms::lognormal(), Gamma(link = "log") or brms::weibull(), or a family epidist defines itself, such as gengamma().

See also

Other family: epidist_family_model(), epidist_family_model.default(), epidist_family_param(), epidist_family_param.default(), epidist_family_param.gengamma(), gengamma()

Examples

data <- sierra_leone_ebola_data |>
  as_epidist_linelist_data(
    pdate_lwr = "date_of_symptom_onset",
    sdate_lwr = "date_of_sample_tested"
  ) |>
  as_epidist_aggregate_data() |>
  as_epidist_marginal_model()
#> ℹ No primary event upper bound provided, using the primary event lower bound + 1 day as the assumed upper bound.
#> ℹ No secondary event upper bound provided, using the secondary event lower bound + 1 day as the assumed upper bound.
#> ℹ No observation time column provided, using 2015-09-14 as the observation date (the maximum of the secondary event upper bound).
#> ! Setting 2394 relative observation times (`relative_obs_time`) greater than 98
#>   (2x the maximum delay) to Inf.
#> ℹ This improves model efficiency by reducing the number of unique observation
#>   times in the data.
#> ℹ The impact on model accuracy should be negligible because these relative
#>   observation times are high enough to cause very limited right truncation.
#> ℹ The original relative observation times are available in
#>   `orig_relative_obs_time`.
#> ℹ Raise `obs_time_threshold` to avoid this behaviour.
family <- epidist_family(data, family = lognormal())
family
#> 
#> Custom family: marginal_lognormal 
#> Link function: identity 
#> Parameters: mu, sigma 
#>