Get new infections over model time
Arguments
- data
A table of model output, typically the output of
model_default()or similar functions.- compartments_from_susceptible
An optional argument, for a character vector of the names of model compartments into which individuals transition from the "susceptible" compartment, and which are not related to infection. A common example is a compartment for "vaccinated" individuals who are no longer susceptible, but who should also not be counted as infected.
- by_group
A logical representing whether the epidemic size should be returned by demographic group, or whether a single population-wide value is returned.
Value
A table with the same columns as data, but with the
additional variable under compartment, "new_infections", resulting in
additional rows.
Examples
# create a population
uk_population <- 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,
time_end = 200,
increment = 1
)
new_infections(data)
#> Key: <time, demography_group>
#> time demography_group new_infections
#> <num> <char> <num>
#> 1: 0 demo_group_1 0.0000
#> 2: 1 demo_group_1 255.6554
#> 3: 2 demo_group_1 597.4504
#> 4: 3 demo_group_1 786.9596
#> 5: 4 demo_group_1 899.2263
#> ---
#> 197: 196 demo_group_1 194151.2197
#> 198: 197 demo_group_1 196154.0970
#> 199: 198 demo_group_1 198089.5442
#> 200: 199 demo_group_1 199954.3897
#> 201: 200 demo_group_1 201745.5414