BatchRun: Run multiple cohorts in a batch

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

Run multiple cohorts in a batch

Description

Runs multiple cohorts in one batch, based on the data in .data.batch

Usage

BatchRun(
  countries = -1,
  coverage = -1,
  agevac = -1,
  agecohort = -1,
  canc.inc = "2020",
  sens = -1,
  unwpp_mortality = TRUE,
  year_born = -1,
  year_vac = -1,
  runs = 1,
  vaccine_efficacy_beforesexdebut = 1,
  vaccine_efficacy_aftersexdebut = 0,
  log = -1,
  by_calendaryear = FALSE,
  use_proportions = TRUE,
  analyseCosts = FALSE,
  canc.cost = "unadj",
  discounting = FALSE,
  disc.cost = 0.03,
  disc.ben = 0.03,
  psa = 0,
  psa_vals = ".data.batch.psa",
  disability.weights = "gbd_2017",
  wb.indicator = "NY.GDP.PCAP.PP.CD",
  wb.year = 2017,
  vaccine = "4vHPV"
)

Arguments

countries	ignore, read from .data.batch
coverage	ignore, read from .data.batch
agevac	ignore, read from .data.batch
agecohort	ignore, read from .data.batch
canc.inc	year from where incidence data is read (2018; old data: 2012) – with updated 2018 Globocan data, DALY weights from GBD, and DALY estimation based on prevalence instead of age of incidence
sens	ignore, does not do anything anymore
unwpp_mortality	logical, whether to create lifetables based on UNWPP mortality estimates or WHO data
year_born	ignore
year_vac	ignore
runs	ignore
vaccine_efficacy_beforesexdebut	vaccine efficacy before sexual debut
vaccine_efficacy_aftersexdebut	vaccine efficacy after sexual debut
log	name of log file
by_calendaryear	logical, output values by calendar year or by year of birth cohort
use_proportions	logical, output data as rates per capita or in totals
analyseCosts	logical, directly run cost-effectiveness analysis on output or not
canc.cost	Character (optional): Is cost of cancer adjusted ("adj" for International $) or not ("unadj" for US$)
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)
psa	integer, number of runs for probabilistic sensitivity analysis (PSA)
psa_vals	data table with values to use in probabilistic sensitivity analysis, usually .data.batch.psa, generated by RegisterBatchData* functions (currently only RegisterBatchDataVimc)
disability.weights	character, disability weights for cervical cancer from GBD 2017 or GBD 2001
wb.indicator	character, World Bank indicator for GDP/GNI per capita in I$/US$ and current/constant data
wb.year	numeric, year of the World Bank indicator value
vaccine	character, bivalent/quadrivalent (4vHPV) or nonavalent (9vHPV) vaccine

Value

Returns combined results

Examples

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lshtm-vimc/prime documentation built on April 21, 2024, 3:21 a.m.