run_onevax_xvwr: 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 eligible for revaccination (R), and return to the R stratum

Description

run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination (R), and return to the R stratum

Usage

run_onevax_xvwr(
  tt,
  gono_params,
  init_params = NULL,
  dur = 1000,
  vea = 0,
  vei = 0,
  ved = 0,
  ves = 0,
  dur_revax = dur,
  vea_revax = vea,
  vei_revax = vei,
  ved_revax = ved,
  ves_revax = ves,
  vbe = 0,
  n_diag_rec = 1,
  primary_uptake = 0,
  booster_uptake = primary_uptake,
  strategy = NULL,
  t_stop = 99
)

Arguments

tt	a numeric vector of times at which the model state is output
gono_params	list of gono params
init_params	A list of starting conditions
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)
dur_revax	scalar or numeric vector with same length as 'gono_params' giving duration of protection for revaccination, default to same as primary
vea_revax	scalar or numeric vector with same length as 'gono_params' giving efficacy of revaccination against acquisition, default to same as primary
vei_revax	scalar or numeric vector with same length as 'gono_params' giving efficacy of revaccination against infectiousness, default to same as primary
ved_revax	scalar or numeric vector with same length as 'gono_params' giving efficacy of revaccination against duration of infection, default to same as primary
ves_revax	scalar or numeric vector with same length as 'gono_params' giving efficacy of revaccination against symptoms, default to same as primary
vbe	scalar indicating pc of population vaccinated before entry (between 0-1)
n_diag_rec	integer for the number of diagnosis history substrata
primary_uptake	scalar or numeric vector with same length as 'gono_params' giving proportion of population undertaking primary vaccination as part of strategy
booster_uptake	scalar or numeric vector with same length as 'gono_params' giving proportion of population undertaking booster vaccination after primary vaccination protection has waned. Defaults to supplied value of 'primary_uptake'. @param n_diag_rec integer for the number of diagnosis history substrata
strategy	single character string in "VoD", "VoD(H)", "VoA", "VoA(H)", "VoD(L)+VoA(H)". Defaults to NULL i.e. no vaccination
t_stop	time at which vaccination should stop (years)

Value

A list of transformed model outputs

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