EpiModel (version 2.3.2)

epi_trackers: Function to run the user-provided epi trackers

Description

see the "Working with Custom Attributes and Summary Statistics in EpiModel" vignette.

Usage

epi_trackers(dat)

Value

The updated dat main list object.

Arguments

dat

Main list object containing a networkDynamic object and other initialization information passed from netsim.

The <code>tracker.list</code> list

.tracker.list is a list of NAMED functions stored in the control list of the dat main list object.

Tracker Functions

This function will apply the tracker functions present in the control list .tracker.list. Each tracker must be a function with EXACTLY one argument: the dat main list object. They must return a VALUE of length one (numeric, logical or character).

See Also

netsim

Examples

if (FALSE) {

# Create some trackers
epi_prop_infected <- function(dat) {
  # we need two attributes for our calculation: `status` and `active`
  needed_attributes <- c("status", "active")
  # we use `with` to simplify code
  output <- with(EpiModel::get_attr_list(dat, needed_attributes), {
    pop <- active == 1             # we only look at active nodes
    cond <- status == "i"   # which are infected
    # how many are `infected` among the `active`
    sum(cond & pop, na.rm = TRUE) / sum(pop, na.rm = TRUE)
  })
  return(output)
}

epi_s_num <- function(dat) {
  needed_attributes <- c("status")
  output <- with(get_attr_list(dat, needed_attributes), {
    sum(status == "s", na.rm = TRUE)
  })
  return(output)
}

# Store the trackers in a named list. The names will be used as column names
# for in the `epi` list
some.trackers <- list(
  prop_infected = epi_prop_infected,
  s_num         = epi_s_num
)

# Make a simple SI model with custom trackers
control <- EpiModel::control.net(
  type = "SI",
  nsims = 1,
  nsteps = 50,
  verbose = FALSE,
  .tracker.list = some.trackers
)

param <- EpiModel::param.net(
  inf.prob = 0.3,
  act.rate = 0.1
)

nw <- network_initialize(n = 50)
nw <- set_vertex_attribute(nw, "race", rbinom(50, 1, 0.5))
est <- EpiModel::netest(
  nw,
  formation = ~edges,
  target.stats = 25,
  coef.diss = dissolution_coefs(~offset(edges), 10, 0),
  verbose = FALSE
)

init <- EpiModel::init.net(i.num = 10)
sim <- EpiModel::netsim(est, param, init, control)

d <- as.data.frame(sim)
d
}