netsim_swfcalib_output: Function to run an EpiModel sim with the result of an...

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

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

Description

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,
  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.
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)
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.

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.

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