Epidemic Model Control Settings — control

Sets the controls for stochastic network models simulated with netsim.

Usage

control_mgen(
  simno = 1,
  nsims = 1,
  ncores = 1,
  nsteps = 10,
  start = 1,
  cumulative.edgelist = FALSE,
  resimulate.network = TRUE,
  truncate.el.cuml = 0,
  amr.FUN = amr_mgen,
  initialize.FUN = initialize_mgen,
  infection.FUN = transmit_mgen,
  progress.FUN = progress_mgen,
  prevalence.FUN = trackers_mgen,
  resim_nets.FUN = resim_nets_mgen,
  summary_nets.FUN = summary_nets,
  tx.FUN = tx_mgen,
  verbose.FUN = verbose.net,
  cleanup.FUN = cleanup_msm,
  save.nwstats = FALSE,
  nwstats.formula = "formation",
  tergmLite = TRUE,
  save.network = FALSE,
  tergmLite.track.duration = FALSE,
  set.control.ergm = control.simulate.formula(MCMC.burnin = 2e+05),
  set.control.tergm = control.simulate.formula.tergm(MCMC.burnin.min = 5000),
  save.other = c("attr", "temp", "el", "net_attr"),
  verbose = FALSE,
  dat.updates = resimnet_updates,
  ...
)

Arguments

simno: Unique ID for the simulation run, used for file naming purposes if used with the EpiModelHPC package.
nsims: Number of simulations to run overall.
ncores: Number of parallel cores per run, if parallel processing is used.
nsteps: Number of time steps per simulation.
start: Starting time step for simulation, with default to 1 to run new simulation. This may also be set to 1 greater than the final time step of a previous simulation to resume the simulation with different parameters.
cumulative.edgelist: If TRUE, models tracks a cumulative edgelist (a historical list of all partners within each network over time), useful for partner services models.
truncate.el.cuml: Number of time steps of the cumulative edgelist to retain. See help file for EpiModel::update_cumulative_edgelist for details
initialize.FUN: Module function to use for initialization of the epidemic model.
resim_nets.FUN: Module function for network resimulation at each time step.
summary_nets.FUN: Module function for network statistic extraction at each time step.
verbose.FUN: Module function to print model progress to the console or external text files.
cleanup.FUN: Module function to tidy the netsim_dat object at the end of each step.
save.nwstats: Calculate and save network statistics as defined in the simnet modules.
nwstats.formula: Right-hand side formula for network statistics to monitor, with default "formation" equal to the model formula. Supports multilayer specification.
tergmLite: Logical indicating usage of tergmLite (non-modifiable currently for EpiModelHIV).
save.network: If TRUE, networkLite object is saved at simulation end.
tergmLite.track.duration: If TRUE, track duration information for models in tergmLite simulations. Supports multilayer specification.
set.control.ergm: Control arguments passed to ergm's simulate_formula.network. Supports multilayer specification.
set.control.tergm: Control arguments passed to tergm's simulate_formula.network. Supports multilayer specification.
save.other: A character vector of elements on the main netsim_dat data object to save out after each simulation.
verbose: If TRUE, print out simulation progress to the console if in interactive mode or text files if in batch mode.
dat.updates: See the general documentation for dat.updates at EpiModel::control.net. The standard implementation for the current MSM model is found in standard_resimnet_updates.
...: Additional arguments passed to the function.
aging.FUN: Module function for aging.
departure.FUN: Module function for general and disease-related departures.
arrival.FUN: Module function for entries into the sexually active population.
partident.FUN: Module function for partner identification process.
acts.FUN: Module function to simulate the number of sexual acts within partnerships.
condoms.FUN: Module function to simulate condom use within acts.
prev.FUN: Module function to calculate prevalence summary statistics.

Value

A list object of class control.net, which can be passed to the EpiModel function netsim.