Get Or Set Model Prior Parameterizations

S4 getter and replacement methods for prior parameterizations on a SeverityEstimateModel, plus chainable set_* helpers for pipeline ergonomics.

Usage

active_prior(x)

active_prior(x) <- value

# S4 method for class 'SeverityEstimateModel'
active_prior(x)

# S4 method for class 'SeverityEstimateModel'
active_prior(x) <- value

set_active_prior(model, ...)

passive_asymptomatic_prior(x)

passive_asymptomatic_prior(x) <- value

# S4 method for class 'SeverityEstimateModel'
passive_asymptomatic_prior(x)

# S4 method for class 'SeverityEstimateModel'
passive_asymptomatic_prior(x) <- value

set_passive_asymptomatic_prior(model, ...)

passive_symptomatic_prior(x)

passive_symptomatic_prior(x) <- value

# S4 method for class 'SeverityEstimateModel'
passive_symptomatic_prior(x)

# S4 method for class 'SeverityEstimateModel'
passive_symptomatic_prior(x) <- value

set_passive_symptomatic_prior(model, ...)

Arguments

x

A SeverityEstimateModel.

value

A named list or named numeric vector providing a beta parameterization. Must be one of alpha/beta, mean/var, mean/sd, mean/concentration.

model

A SeverityEstimateModel.

...

Beta distribution parameterization. Must be one of alpha/beta, mean/var, mean/sd, mean/concentration.

Value

active_prior(x) returns the current active prior parameterization. If the active prior has not yet been set, a warning is issued and the default prior c(alpha = 1.0, beta = 1.0) is returned.

active_prior(x) <- value returns x modified to contain the active prior parameterization.

set_active_prior(model, ...) returns model modified to contain the active prior parameterization.

passive_asymptomatic_prior(x) returns the current passive asymptomatic prior parameterization. If the passive asymptomatic prior has not yet been set, a warning is issued and the default prior c(alpha = 1.0, beta = 1.0) is returned.

passive_asymptomatic_prior(x) <- value returns x modified to contain the passive asymptomatic prior parameterization.

set_passive_asymptomatic_prior(model, ...) returns model modified to contain the passive asymptomatic prior parameterization.

passive_symptomatic_prior(x) returns the current passive symptomatic prior parameterization. If the passive symptomatic prior has not yet been set, a warning is issued and the default prior c(alpha = 1.0, beta = 1.0) is returned.

passive_symptomatic_prior(x) <- value returns x modified to contain the passive symptomatic prior parameterization.

set_passive_symptomatic_prior(model, ...) returns model modified to contain the passive symptomatic prior parameterization.

Examples

line_list <- data.frame(
  patient = 1L:3L,
  week = c(1L, 1L, 2L),
  age = c("Youth", "Adult", "Senior"),
  detection = c("Active", "Passive", "Active"),
  outcome = c("Asymptomatic", "Death", "Symptomatic")
)
population <- data.frame(
  age = c("Youth", "Adult", "Senior"),
  amount = rep(987L, 3L)
)
model <- SeverityEstimateModel(line_list, population) |>
  set_active_prior(mean = 0.9, concentration = 12.5) |>
  set_passive_asymptomatic_prior(alpha = 1.0, beta = 1.0) |>
  set_passive_symptomatic_prior(mean = 0.1, var = 0.0064)
model
#> Severity Estimate Model:
#> 
#> Data:
#>     dataset rows columns
#>   line_list    3       5
#>  population    3       2
#> 
#> Detection Probability Priors:
#>   active prior: beta(11.25, 1.25)
#>   passive_asymptomatic prior: beta(1.0, 1.0)
#>   passive_symptomatic prior: beta(1.306, 11.76)
#> 
#> Timesteps:
#>   not set
#> 
#> Detection:
#>   not set
#> 
#> Outcome:
#>   not set
#> 
#> Strata:
#>   none