netsim_scenarios: Function to run EpiModel network simulations with scenarios

In statnet/EpiModelHPC: EpiModel Extensions for High-Performance Computing

Function to run EpiModel network simulations with scenarios

Description

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,
  save_pattern = "simple"
)

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.
init	Initial conditions, as an object of class init.net.
control	Control settings, as an object of class control.net.
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)
save_pattern	A character vector of what should be kept in the final netsim objects. It can contain the names of the elements as well as: "simple" (defautlt) to only keep "epi", "param" and "control"; "restart" to get the elements required to restart from such file; "all" to not trim the object at all. c("simple", "el.cuml") is an example of a valid pattern to save "epi", "param", "control" and "el.cuml". If control$raw.output is TRUE, this parameter has no effect and the full result is saved.

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.

statnet/EpiModelHPC documentation built on Nov. 13, 2023, 11:38 a.m.