Get Or Set Model Detection Mapping

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

Usage

detection(x)

detection(x) <- value

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

has_detection(x)

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

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

require_detection(model, mode = "error")

set_detection(model, name, map = c(active = "active", passive = "passive"))

Arguments

x

A SeverityEstimateModel.

value

A named list with entries name and map.

model

A SeverityEstimateModel.

mode

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

name

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

map

A named character vector mapping detection column values to either active or passive.

Value

detection(x) returns the current detection specification.

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

has_detection(x) returns TRUE if detection has been set, FALSE otherwise.

require_detection(model, mode) returns model. If detection is unset, the behavior depends on mode.

set_detection(model, ...) returns model modified to include the detection 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_detection(
    "detection",
    map = c("Active" = "active", "Passive" = "passive")
  )
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:
#>   column: detection
#>     active: 2 cases (values: Active)
#>     passive: 1 cases (values: Passive)
#> 
#> Outcome:
#>   not set
#> 
#> Strata:
#>   none