Get the epidemic size — epidemic

Get the size of the epidemic at any stage between the start and the end. This is calculated as the number of individuals recovered from infection at that stage of the epidemic.

Usage

epidemic_size(
  data,
  stage = 1,
  time = NULL,
  by_group = TRUE,
  include_deaths = FALSE,
  simplify = TRUE
)

Arguments

data: A table of model output, typically the output of model_de ault() or similar functions.
stage: A numeric vector for the stage of the epidemic at which to return the epidemic size; here 0.0 represents the start time of the epidemic i.e., the initial conditions of the epidemic simulation, while 1.0 represents the end of the epidemic simulation model (100% of model time). Defaults to 1.0, at which stage returned values represent the final size of the epidemic. This value is overridden by any values passed to the time argument.
time: Alternative to stage, an integer-like vector for the timepoint of the epidemic at which to return the epidemic size. Overrides any values passed to stage.
by_group: A logical representing whether the epidemic size should be returned by demographic group, or whether a single population-wide value is returned. Defaults to TRUE.
include_deaths: A logical value that indicates whether to count dead individuals in the epidemic size calculation. Defaults to FALSE. Setting include_deaths = TRUE makes the function look for a "dead" compartment in the data. If there is no such column, the function returns only the final number of recovered or removed individuals in each demographic group.
simplify: A logical determining whether the epidemic size data should be simplified to a vector with one element for each demographic group. If the length of stage or time is $>$ 1, this argument is overridden and the data are returned as a <data.table>.

Value

If simplify == TRUE and a single timepoint is requested, returns a vector of epidemic sizes of the same length as the number of demographic groups. If by_group == FALSE, sums the epidemic size to return an overall value for the full population.

If multiple timepoints are requested, or if multiple replicates are present under a specially named column "replicate" (only from the Ebola model), no simplification to a vector is possible; returns a <data.table> of timepoints and epidemic sizes at each timepoint.

All options return the absolute sizes and not proportions.

Details

This function can be used to calculate the final size of the epidemic, by setting stage = 1.0 (100% of model time; the default).

The function allows for the calculation of epidemic sizes by demographic group as well as the total epidemic size.

Examples

# create a population
uk_population <- population(
  name = "UK population",
  contact_matrix = matrix(1),
  demography_vector = 67e6,
  initial_conditions = matrix(
    c(0.9999, 0.0001, 0, 0, 0),
    nrow = 1, ncol = 5L
  )
)

# run epidemic simulation with no vaccination or intervention
data <- model_default(
  population = uk_population
)

# get the final epidemic size if no other arguments are specified
epidemic_size(data)
#> [1] 481200.2

# get the epidemic size at the halfway point
epidemic_size(data, stage = 0.5)
#> [1] 81921.88

# alternatively, get the epidemic size at `time = 50`
epidemic_size(data, time = 50)
#> epidemic_size(): `time` provided will override any `stage` provided
#> [1] 81921.88