run_onevax_xpvwrh: run model with a two-dose vaccine for input parameter sets,...

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

run model with a two-dose 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, those with waned partial vaccines return to the unvaccinated stratum (X) and considered immunologically naive. A user defined proportion of the population is vaccine hesitant and is never vaccinated. Full acciantion (V) with 2 doses gives maximum protection whereas partial vaccination with 1 dose (P) gives less. Individuals can get 2 doses either by committing in X or upon visiting a clinic in P.

Description

run model with a two-dose 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, those with waned partial vaccines return to the unvaccinated stratum (X) and considered immunologically naive. A user defined proportion of the population is vaccine hesitant and is never vaccinated. Full acciantion (V) with 2 doses gives maximum protection whereas partial vaccination with 1 dose (P) gives less. Individuals can get 2 doses either by committing in X or upon visiting a clinic in P.

Usage

run_onevax_xpvwrh(
  tt,
  gono_params,
  init_params = NULL,
  dur_v = 1000,
  dur_p = dur_v,
  vea = 0,
  vei = 0,
  ved = 0,
  ves = 0,
  dur_revax = dur_v,
  vea_revax = vea,
  vei_revax = vei,
  ved_revax = ved,
  ves_revax = ves,
  vea_p = vea,
  vei_p = vei,
  ved_p = ved,
  ves_p = ves,
  vbe = 0,
  r1 = 0,
  r2 = 0,
  r2_p = 0,
  booster_uptake = (r1 * r2),
  strategy = NULL,
  t_stop = 99,
  hes = 0,
  n_erlang = 1,
  n_diag_rec = 1,
  years_history = 1
)

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_v	duration of time spent in V stratum after completing a round of primary vaccination (fully vaccinated, accepting first and second dose)
dur_p	duration of time spent in the P stratum, partially vaccinated (accepting only the first dose)
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
vea_p	scalar indicating efficacy of partial vaccination against acquisition (between 0-1)
vei_p	scalar indicating efficacy of partial vaccination against infectiousness (between 0-1)
ved_p	scalar indicating efficacy of partial vaccination against duration (between 0-1)
ves_p	scalar indicating efficacy of partial vaccination against symptoms (between 0-1)
vbe	scalar indicating pc of population vaccinated before entry (between 0-1)
r1	scalar or numeric vector with same length as 'gono_params' giving proportion of population offered vaccine only accepting the first dose, becoming partially vaccinated
r2	scalar or numeric vector with same length as 'gono_params' giving proportion of the population who accepted the first dose of the vaccine who go on to accept the second dose, becoming fully vaccinated
r2_p	scalar or numeric vector with same length as 'gono_params' giving proportion of partially vaccinated individuals who later receive a second dose when returning to the clinic due to screening or illness
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 r1 * r2
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)
hes	Proportion of individuals in the population who are vaccine hesitant
n_erlang	integer giving the number of erlang vaccination transitions through vaccine-protected strata until that protection has waned
n_diag_rec	integer for the number of diagnosis history substrata
years_history	number of years that diagnosis history is recorded for

Value

A list of transformed model outputs

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