Get Or Set Model Stratifications — strata • SeverityEstimate

S4 getter and replacement methods for the strata slot on a SeverityEstimateModel, plus a chainable set_strata() helper for pipeline ergonomics.

Usage

strata(x)

strata(x) <- value

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

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

set_strata(model, name, levels = NULL, degrees_of_freedom = NULL)

Arguments

x: A SeverityEstimateModel.
value: A named list with entries name, levels, and degrees_of_freedom.
model: A SeverityEstimateModel.
name: The name of the stratification column, which must be present in both the line_list and population data.frames.
levels: The levels for the stratification, or NULL to infer from line_list/population.
degrees_of_freedom: The degrees of freedom for the strata fixed effects. NULL and 0L use unsmoothed categorical effects. Values greater than 0L request an ordered smooth effect and therefore require explicit levels. The value must be less than the saturated categorical fit, i.e. at most length(levels) - 2L.

Value

strata(x) returns the current list of model stratifications.

strata(x) <- value returns x modified to include the given stratification.

set_strata(model, ...) returns model modified to include the given stratification.

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_strata("age", levels = c("Youth", "Adult", "Senior"))
model
#> Formal class 'SeverityEstimateModel' [package "SeverityEstimate"] with 9 slots
#>   ..@ line_list                 :'data.frame':	3 obs. of  5 variables:
#>   .. ..$ patient  : int [1:3] 1 2 3
#>   .. ..$ week     : int [1:3] 1 1 2
#>   .. ..$ age      : chr [1:3] "Youth" "Adult" "Senior"
#>   .. ..$ detection: chr [1:3] "Active" "Passive" "Active"
#>   .. ..$ outcome  : chr [1:3] "Asymptomatic" "Death" "Symptomatic"
#>   ..@ population                :'data.frame':	3 obs. of  2 variables:
#>   .. ..$ age   : chr [1:3] "Youth" "Adult" "Senior"
#>   .. ..$ amount: int [1:3] 987 987 987
#>   ..@ strata                    :List of 1
#>   .. ..$ :List of 3
#>   .. .. ..$ name              : chr "age"
#>   .. .. ..$ levels            : chr [1:3] "Youth" "Adult" "Senior"
#>   .. .. ..$ degrees_of_freedom: int 0
#>   ..@ timesteps                 : list()
#>   ..@ detection                 : list()
#>   ..@ outcome                   : list()
#>   ..@ active_prior              : num(0) 
#>   ..@ passive_asymptomatic_prior: num(0) 
#>   ..@ passive_symptomatic_prior : num(0)