EmulateVaccineImpactVimcStochastic_all_cecx_burden: Emulate vaccine impact estimates (VIMC stochastic runs) - all...

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

Emulate vaccine impact estimates (VIMC stochastic runs) - all cervical cancer burden

Description

Emulate vaccine impact estimates for VIMC stochastic runs/sensitivity analysis. The inputs are central disease burden estimates, input parameter distributions (latin hyper sampling), runs for sensitivity analysis, and filename for stochastic burden estimates. The outputs are stochastic disease burden estimates – all cervical cancer burden. (full results file plus a file per country).

Usage

EmulateVaccineImpactVimcStochastic_all_cecx_burden(
  disease_burden_template_file,
  centralBurdenResultsFile,
  centralBurdenResultsFile_all_cecx_burden,
  central_disease_burden_file_all,
  batch_cohort_file,
  psaData,
  diseaseBurdenStochasticFile_all_cecx_burden,
  diseaseBurden_central_StochasticFile_all_cecx_burden,
  psa_runs,
  countryCodes = -1,
  vaccination_scenario
)

Arguments

disease_burden_template_file	csv file (required), central disease burden template (vimc format); add column with run_id to get stochastic disease burden template
centralBurdenResultsFile	csv file (required), central disease burden estimates pre and post vaccination (HPV 16/18 types)
centralBurdenResultsFile_all_cecx_burden	csv file (required), central disease burden estimates pre and post vaccination (all HPV types)
central_disease_burden_file_all	csv file (required), central disease burden estimates (vimc format)
psaData	data table (required), latin hyper cube sample of input parameters
diseaseBurdenStochasticFile_all_cecx_burden	character string (required), stochastic disease burden estimates file(s) (output) - all cervical cancer burden
diseaseBurden_central_StochasticFile_all_cecx_burden	character string (required), (central + 95 (output) - all cervical cancer burden
psa_runs	integer (required), simulation runs for sensitivity analysis
countryCodes	list (optional), If country codes are provided, stochastic burden estimates are generated for these countries. If set to -1, then stochastic burden estimates are generated for the countries included in the central burden estimates.
vaccination_scenario	logical (required), generate stochastic burden estimates for (vaccination) or (no vaccination) scenario

Details

Stochastic disease burden estimates are generated. (i) full results files 1 full results file for pre-vaccination (optional) 1 full results file for post-vaccination (ii) 1 file per country for all runs 1 file per country for all runs – pre-vaccination (optional) 1 file per country for all runs – post-vaccination

Value

Null return value; disease burden estimates are saved to corresponding files

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