Get Or Set Model Outcome Mapping

S4 getter and replacement methods for the outcome slot on a SeverityEstimateModel, plus chainable helpers to set and validate outcome readiness.

Usage

outcome(x)

outcome(x) <- value

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

has_outcome(x)

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

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

require_outcome(model, mode = "error")

set_outcome(
  model,
  name,
  map = c(asymptomatic = "asymptomatic", symptomatic = "symptomatic", severe = "severe")
)

Arguments

x

A SeverityEstimateModel.

value

A named list with entries name and map.

model

A SeverityEstimateModel.

mode

How require_outcome() should respond when outcome is not set. One of error, warn, silent.

name

The name of the outcome column, which must be present in line_list.

map

A named character vector mapping outcome column values to one of asymptomatic, symptomatic, or severe.

Value

outcome(x) returns the current outcome specification.

outcome(x) <- value returns x modified to include the outcome specification.

has_outcome(x) returns TRUE if outcome has been set, FALSE otherwise.

require_outcome(model, mode) returns model. If outcome is unset, the behavior depends on mode.

set_outcome(model, ...) returns model modified to include the outcome specification.

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_outcome("outcome", map = c(
    "Asymptomatic" = "asymptomatic",
    "Symptomatic" = "symptomatic",
    "Death" = "severe"
  ))
model
#> Severity Estimate Model:
#> 
#> Data:
#>     dataset rows columns
#>   line_list    3       5
#>  population    3       2
#> 
#> Detection Probability Priors:
#>   active prior: beta(1.0, 1.0) (default)
#>   passive_asymptomatic prior: beta(1.0, 1.0) (default)
#>   passive_symptomatic prior: beta(1.0, 1.0) (default)
#> 
#> Timesteps:
#>   not set
#> 
#> Detection:
#>   not set
#> 
#> Outcome:
#>   column: outcome
#>     asymptomatic: 1 cases (values: Asymptomatic)
#>     symptomatic: 1 cases (values: Symptomatic)
#>     severe: 1 cases (values: Death)
#> 
#> Strata:
#>   none