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Function to run an EpiModel sim with the result of an swfcalib calibration

Source: R/swfcalib_helpers.R
netsim_swfcalib_output.Rd

Function to run an EpiModel sim with the result of an swfcalib calibration

Usage

netsim_swfcalib_output(
  path_to_x,
  param,
  init,
  control,
  calib_object,
  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.

calib_object

a formatted calibration object

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)

Value

a template function to be used by add_workflow_step

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.

Step Template

Step Templates are helper functions to be used within add_workflow_step. Some basic ones are provided by the slurmworkflow package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. Additional Step Templates can be created to simplify specific tasks. The easiest way to do so is as wrappers around existing templates.