control_cl: Epidemic Model Control Settings

In statnet/PrEP-for-ASMM-and-adult-MSM: Network-Based Epidemic Modeling of HIV Transmission among MSM and ASMM populations

Description

Sets the controls for stochastic network models simulated with netsim.

Usage

control_cl(simno = 1, nsims = 1, ncores = 1, nsteps = 100,
  start = 1, initialize.FUN = initialize_camplc,
  followUP.FUN = FU_elements_camplc, aging.FUN = aging_camplc,
  deaths.FUN = deaths_msm, births.FUN = births_camplc,
  outdebut.FUN = out_debut_camplc, test.FUN = test_msm,
  tx.FUN = tx_msm, prep.FUN = prep_msm, prep2.FUN = prep_adol,
  prep.classtrans.FUN = prep_adherence_trans,
  progress.FUN = progress_msm, agemixing.FUN = agemix_campcl,
  vl.FUN = vl_msm, aiclass.FUN = NULL, roleclass.FUN = NULL,
  role.classtrans.FUN = roleclass_trans, resim_nets.FUN = simnet_msm,
  disclose.FUN = disclose_msm, acts.FUN = acts_msm,
  condoms.FUN = condoms_msm, riskhist.FUN = riskhist_msm,
  riskhistasmm.FUN = riskhist_adol, position.FUN = position_msm,
  trans.FUN = trans_msm, prev.FUN = prevalence_msm,
  verbose.FUN = verbose_msm, save.nwstats = FALSE,
  save.other = c("attr", "temp", "riskh", "el", "p", "riskhist",
  "age.inf.vec", "el.age"), verbose = TRUE, verbose.int = 1, ...)

Arguments

simno	Unique ID for the simulation run, used for file naming purposes if used in conjunction with the EpiModelHPC package.
nsims	Number of simulations.
ncores	Number of cores per run, if parallelization is used within the EpiModelHPC package.
nsteps	Number of time steps per simulation.
start	Starting time step for simulation, with default to 1 to run new simulation. This may also be set to 1 greater than the final time step of a previous simulation to resume the simulation with different parameters.
initialize.FUN	Module function to use for initialization of the epidemic model.
followUP.FUN	re-create tracking elements of dat (riskhist, age.inf.vec and counts)
aging.FUN	Module function for aging.
deaths.FUN	Module function for general and disease-realted deaths.
births.FUN	Module function for births or entries into the population.
outdebut.FUN	Module for outing into the population and debuting as sexually available
test.FUN	Module function for diagnostic disease testing.
tx.FUN	Module function for ART initiation and adherence.
prep.FUN	Module function for PrEP initiation and utilization.
prep2.FUN	Module function for PrEP initiation and utilization for ASMM
prep.classtrans.FUN	Model for transmisioning PrEP adherence class from ASMM to adult MSM at age 19
progress.FUN	Module function for HIV disease progression.
vl.FUN	Module function for HIV viral load evolution.
aiclass.FUN	Module function for one-off AI risk class transitions.
roleclass.FUN	Module function for transitions in sexual roles.
resim_nets.FUN	Module function for network resimulation at each time step.
disclose.FUN	Module function for HIV status disclosure.
acts.FUN	Module function to simulate the number of sexual acts within partnerships.
condoms.FUN	Module function to simulate condom use within acts.
riskhist.FUN	Module function to calculate risk history for uninfected persons in the population.
riskhistasmm.FUN	Module function to calculate simplified risk history for uninfected persons in the population.
position.FUN	Module function to simulate sexual position within acts.
trans.FUN	Module function to stochastically simulate disease transmission over acts given individual and dyadic attributes.
prev.FUN	Module function to calculate prevalence summary statistics.
verbose.FUN	Module function to print model progress to the console or external text files.
save.nwstats	Calculate and save network statistics as defined in the simnet modules.
save.other	Character vector containing other list elements of dat to save.
verbose	If TRUE, print out simulation progress to the console if in interactive mode or text files if in batch mode.
verbose.int	Integer specifying the interval between time steps at which progress is printed.
...	Additional arguments passed to the function.
roleclasstrans.FUN	Module function for transitioning the I,R,V distribution from asmm to MSM.

Value

A list object of class control_msm, which can be passed to the EpiModel function netsim.

statnet/PrEP-for-ASMM-and-adult-MSM documentation built on June 22, 2019, 12:45 a.m.