RunCohort: Run PRIME for a single birth-cohort

In lshtm-vimc/prime: PRIME -- Papillomavirus Rapid Interface for Modelling and Economics

Run PRIME for a single birth-cohort

Description

Runs PRIME for one birth-cohort. Usually called by another function such as RunCountry().

Usage

RunCohort(
  lifetab,
  cohort,
  incidence,
  mortality_cecx,
  prevalence,
  agevac,
  coverage,
  campaigns,
  vaccine_efficacy_nosexdebut,
  vaccine_efficacy_sexdebut,
  cost_cancer,
  discounting = FALSE,
  disc.cost = 0.03,
  disc.ben = 0.03,
  country_iso3 = NULL,
  run_country = FALSE,
  disability.weights = "gbd_2017"
)

Arguments

lifetab	Data.table: The life-table for this cohort. Can be created using the lifeTable() function.
cohort	Number: The cohort-size of this birth-cohort at the time where the lifetable starts.
incidence	Numeric vector: Age-specific CeCx(16/18) incidence-rates.
mortality_cecx	Numeric vector: Age-specific CeCx(16/18) mortality-rates.
prevalence	Numeric vector: Age-specific CeCx(16/18) prevalence rates (5-year prevalence) – referring to people who are alive within 5 years of diagnosis.
agevac	Number: Age at which the cohort is vaccinated.
coverage	Number: Proportion of the cohort that will receive a vaccination.
campaigns	List or number: MAC cohort-vaccinations (needs to be changed).
vaccine_efficacy_nosexdebut	Number: proportion indicating vaccine-efficacy before sexual debut.
vaccine_efficacy_sexdebut	Number: proportion indicating vaccine-efficacy after sexual debut.
cost_cancer	Number: total per capita cost of cancer.
discounting	Logical (optional): If TRUE, run cost-effectiveness analysis undiscounted and discounted. If FALSE, only uses undiscounted
disc.cost	Number (optional): Discounting for health costs (only if discounting=TRUE)
disc.ben	Number (optional): Discounting for health outcomes (only if discounting=TRUE)

Value

Returns a data.table with size of the birth-cohort and age-specific incidence-rates, mortality-rates, years-of-life-lost, years-of-healthy-life-lost, and cancer-costs before and after vaccination. Also displays whether discounting has been used ("type" column).

Examples

lifetab <- lifeTable(unlist(data.mortall[iso3=="AFG",
  as.character(0:100), with=FALSE], use.names=FALSE), 9)
cohort <- -1
incidence <- unlist(data.incidence[iso3=="AFG", as.character(0:100), with=FALSE],
  use.names=FALSE)
mortality_cecx <- unlist(data.mortall[iso3=="AFG", as.character(0:100), with=FALSE],
  use.names=FALSE)
prevalence <- unlist(data.cecx_5y_prevalence[iso3=="AFG",
  as.character(0:100), with=FALSE], use.names=FALSE)
agevac <- 9
coverage <- 0.8
campaigns <- -1
vaccine_efficacy_nosexdebut <- 0.95
vaccine_efficacy_sexdebut <- 0
cost_cancer <- 100

RunCohort(lifetab, cohort, incidence, mortality_cecx, prevalence, agevac,
  coverage, campaigns, vaccine_efficacy_nosexdebut, vaccine_efficacy_sexdebut,
  cost_cancer, disc.cost=0.03, disc.ben=0.03,
  discounting=FALSE, country_iso3="AFG", run_country=FALSE)

lshtm-vimc/prime documentation built on Feb. 29, 2024, 10:49 a.m.