run_onevax_xvw_trial: Run model with single vaccine for input parameter sets,...

In mrc-ide/gonovax: Deterministic Compartmental Model of Gonorrhoea with Vaccination

Run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are not eligible for re-vaccination.

Description

Run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are not eligible for re-vaccination.

Usage

run_onevax_xvw_trial(
  tt,
  gono_params,
  initial_params_trial = NULL,
  dur = 1000,
  vea = 0,
  vei = 0,
  ved = 0,
  ves = 0,
  p_v = 0.5,
  n_erlang = 1,
  stochastic = FALSE,
  N = 6e+05,
  n_diag_rec = 1,
  asymp_recorded = TRUE
)

Arguments

tt	a numeric vector of times at which the model state is output in years
gono_params	list of gono params for a vaccination trial
initial_params_trial	list of initial conditions for model trial. Set default as NULL.
dur	scalar or numeric vector with same length as 'gono_params' giving duration of the vaccine (in years)
vea	scalar or numeric vector with same length as 'gono_params' giving efficacy of the vaccine against acquisition (between 0-1)
vei	scalar or numeric vector with same length as 'gono_params' giving efficacy of the vaccine against infectiousness (between 0-1)
ved	scalar or numeric vector with same length as 'gono_params' giving efficacy of the vaccine against duration (between 0-1)
ves	scalar or numeric vector with same length as 'gono_params' giving efficacy of the vaccine against symptoms (between 0-1)
p_v	scalar giving proportion of the trial cohort vaccinated, default is 0.5.
n_erlang	integer giving the number of transitions that need to be made
stochastic	logical indicating if the run should be made with the default deterministic trial model in continuous time or stochastic trial model in discrete time
N	integer to assign the total number of individuals in the trial (split equally across the two arms)
n_diag_rec	integer giving the number of each X, V(erlang), and W stratum, allowing tracking of diagnosis history. e.g for a n_diag_rec = 2 and erlang = 1, there will be X.I, X.II, V1.I, V1.II, W.I, W.II strata. Where '.I' corresponds to never-diagnosed individuals and '.II' is for individuals diagnosed at least once.
asymp_recorded	logical indicating if the trial screens for and records asymptomatic diagnosis. If FALSE, asymptomatic infected individuals undergoing treatment do not move diagnosis history stratum

mrc-ide/gonovax documentation built on Dec. 15, 2024, 11:02 a.m.