Step template to run sims with the result of an swfcalib calibration

Step template to run sims with the result of an swfcalib calibration

Usage

step_tmpl_netsim_swfcalib_output(
  path_to_x,
  param,
  init,
  control,
  calib_object,
  n_rep,
  n_cores,
  output_dir,
  libraries = NULL,
  save_pattern = "restart",
  setup_lines = NULL,
  max_array_size = 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.

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.

setup_lines

(optional) a vector of bash lines to be run first. This can be used to load the required modules (like R, python, etc).

max_array_size

maximum number of array jobs to be submitted at the same time. Should be strictly less than the maximum number of jobs you are allowed to submit to slurm on your HPC.

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.