control_het: Control Settings for Stochastic Network Model of HIV-1...

Description Usage Arguments Details

View source: R/params.R

Description

This function sets the control settings for the stochastic network models in the epimethods package.

Usage

1
2
3
4
5
6
7
8
9
control_het(simno = 1, nsteps = 100, start = 1, nsims = 1, ncores = 1,
  par.type = "single", initialize.FUN = initialize_het,
  aging.FUN = aging_het, cd4.FUN = cd4_het, vl.FUN = vl_het,
  dx.FUN = dx_het, tx.FUN = tx_het, deaths.FUN = deaths_het,
  births.FUN = births_het, resim_nets.FUN = simnet_het,
  infection.FUN = infect_het, prev.FUN = prevalence_het,
  verbose.FUN = verbose_het, module.order = NULL, save.nwstats = FALSE,
  save.other = c("el", "attr"), verbose = TRUE, verbose.int = 1,
  skip.check = TRUE, ...)

Arguments

simno

Simulation ID number.

nsteps

Number of time steps to simulate the model over in whatever unit implied by time.unit.

start

Starting time step for simulation

nsims

Number of simulations.

ncores

Number of parallel cores to use for simulation jobs, if using the EpiModel.hpc package.

par.type

Parallelization type, either of "single" for multi-core or "mpi" for multi-node MPI threads.

initialize.FUN

Module to initialize the model at time 1.

aging.FUN

Module to age active nodes.

cd4.FUN

CD4 progression module.

vl.FUN

HIV viral load progression module.

dx.FUN

HIV diagnosis module.

tx.FUN

HIV treatment module.

deaths.FUN

Module to simulate death or exit.

births.FUN

Module to simulate births or entries.

resim_nets.FUN

Module to resimulate the network at each time step.

infection.FUN

Module to simulate disease infection.

prev.FUN

Module to calculate disease prevalence at each time step, with the default function of prevalence_het.

verbose.FUN

Module to print simulation progress to screen, with the default function of verbose_het.

module.order

A character vector of module names that lists modules the order in which they should be evaluated within each time step. If NULL, the modules will be evaluated as follows: first any new modules supplied through ... in the order in which they are listed, then the built-in modules in their order of the function listing. The initialize.FUN will always be run first and the verbose.FUN always last.

save.nwstats

Save out network statistics.

save.other

Other list elements of dat to save out.

verbose

If TRUE, print progress to console.

verbose.int

Interval for printing progress to console.

skip.check

If TRUE, skips the error check for parameter values, initial conditions, and control settings before running the models.

...

Additional arguments passed to the function.

Details

This function sets the parameters for the models.


statnet/EpiModelHIVhet documentation built on May 30, 2019, 9:47 a.m.