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Function to run EpiModel network simulations with scenarios

Source: R/netsim_scenarios.R
netsim_scenarios.Rd

This function will run n_rep replications of each scenarios in the scenarios_list. It runs them as multiple batches of up to n_cores simulations at a time. The simfiles are then stored in the output_dir folder and are named using the following pattern: "sim__name_of_scenario__2.rds". Where the last number is the batch number for this particular scenario. Each scenario is therefore run over ceiling(n_rep / n_cores) batches. This function is meant to mimic the behavior of step_tmpl_netsim_scenarios in your local machine. It should fail in a similar fashion an reciprocally, if it runs correctly locally, moving to an HPC should not produce any issue.

Usage

netsim_scenarios(
  path_to_x,
  param,
  init,
  control,
  scenarios_list,
  n_rep,
  n_cores,
  output_dir,
  libraries = NULL,
  ...
)

Arguments

path_to_x

Path to a Fitted network model object saved with saveRDS. (See the x argument to the EpiModel::netsim function)

param

Model parameters, as an object of class param.net. Includes transmission probability (inf.prob), act rate (act.rate), recovery rate (rec.rate), and demographic rates for models with vital dynamics. Custom parameters for extended models may also be passed through param.net.

init

Initial conditions, as an object of class init.net. Specifies the initial number of infected nodes (i.num) and, for SIR models, recovered nodes (r.num). For two-group models, the corresponding .g2 parameters are also required.

control

Control settings, as an object of class control.net. Key settings include type (disease model: "SI", "SIR", or "SIS"), nsteps (number of time steps), nsims (number of simulations), tergmLite (lightweight mode for performance), and resimulate.network (required for models with vital dynamics). For extended models, custom module functions are also passed here.

scenarios_list

A list of scenarios to be run. Produced by the EpiModel::create_scenario_list function

n_rep

The number of replication to be run for each scenario.

n_cores

The number of CPUs on which the simulations will be run.

output_dir

The folder where the simulation files are to be stored.

libraries

A character vector containing the name of the libraries required for the model to run. (e.g. EpiModelHIV or EpiModelCOVID)

...

for compatibility reasons

Checkpointing

This function takes care of editing .checkpoint.dir to create unique sub directories for each scenario. The EpiModel::control.net way of setting up checkpoints can be used transparently.