Make a Lightweight Restart Point From a netsim Object with tergmLite

Extract the elements required for re-initializing a netsim simulation from a completed simulation. This function also resets the Unique IDs and Time values to reduce the size of the simulation. This function only works for simulations where control$tergmLite = TRUE

Usage

make_restart_point(sim_obj, time_attrs, sim_num = 1, keep_steps = 1)

Arguments

sim_obj: a netsim object from an ended netsim call.
time_attrs: a character vector containing the names of the attributes that are expressed in time-steps. These will be offsetted so the last step in the original simulation become the step 1 (default) in the new ones. If no such attributes exist, pass c().
sim_num: the number of the simulation to extract from the netsim object (default = 1).
keep_steps: The number of simulation steps to keep from the previous run. By default only keep one but more is possible if some back-history is wanted.

Value

a trimed netsim object with only one simulation that is ready to be used as a restart point.

Details

The restart point created always contains a single simulation and drops the attr.history, the raw.records and stats from the initial simulation.

The epi trackers, cumulative edgelists, transmission matrix and nwstats are truncated to only contain the last keep_steps entries.

Warning: the time_attrs argument is mandatory. Almost all simulation worth restarting have such attributes (e.g. time.of.hiv.infection). If no such argument exists, passing c() will allow the function to run while ensuring that this was done on purpose.

When restarting from the output of this function, it is suggested to express the time steps in a relative maner in control.net:

control.net(
  start = restart_point$control$nsteps + 1),
  nsteps = restart_point$control$nsteps + 1 + 104)
)

Examples

if (FALSE) { # \dontrun{
# With  pre-existing `sim`, `param` and `init` object (see `netsim`)

# List all attributes that store a time step
time_attrs <- c(
  "inf.time",
  "stage.time",
  "aids.time",
  "prep.start.last"
)
# Make a restart point a re-run for 10 more timesteps
x <- make_restart_point(sim, time_attrs, sim_num = 1, keep_steps = 1)
control <- control_msm(
  start = x$control$nsteps + 1,
  nsteps = x$control$nsteps + 1 + 10
)
sim <- netsim(x, param, init, control)
} # }