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license: MIT
title: 'vacalibration: Calibration of Computer-Coded Verbal Autopsy Algorithm'
version: '2.2'
doi: 10.32614/CRAN.package.vacalibration
abstract: Calibrates population-level cause-specific mortality fractions (CSMFs) that
  are derived using computer-coded verbal autopsy (CCVA) algorithms. Leveraging the
  data collected in the Child Health and Mortality Prevention Surveillance (CHAMPS;<https://champshealth.org/>)
  project, the package stores misclassification matrix estimates of three CCVA algorithms
  (EAVA, InSilicoVA, and InterVA) and two age groups (neonates aged 0-27 days, and
  children aged 1-59 months) across countries (specific estimates for Bangladesh,
  Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Africa, and a combined
  estimate for all other countries), enabling global calibration. These estimates
  are obtained using the framework proposed in Pramanik et al. (2025;<https://doi.org/10.1214/24-AOAS2006>)
  and are analyzed in Pramanik et al. (2026;<https://doi.org/10.1136/bmjgh-2025-021747>).
  Given VA-only data for an age group, CCVA algorithm, and country, the package utilizes
  the corresponding misclassification matrix estimate in the modular VA-Calibration
  framework (Pramanik et al.,2025;<https://doi.org/10.1214/24-AOAS2006>) and produces
  calibrated estimates of CSMFs. The package also supports ensemble calibration to
  accommodate multiple algorithms. More generally, this allows calibration of population-level
  prevalence derived from single-class predictions of discrete classifiers. For this,
  users need to provide fixed or uncertainty-quantified misclassification matrices.
  This work is supported by the Eunice Kennedy Shriver National Institute of Child
  Health K99 NIH Pathway to Independence Award (1K99HD114884-01A1), the Bill and Melinda
  Gates Foundation (INV-034842), and the Johns Hopkins Data Science and AI Institute.
authors:
- family-names: Pramanik
  given-names: Sandipan
  email: sandy.pramanik@gmail.com
  orcid: https://orcid.org/0000-0002-7196-155X
- family-names: Wilson
  given-names: Emily
  email: wilsonem@gmail.com
- family-names: Fiksel
  given-names: Jacob
  email: jfiksel@gmail.com
- family-names: Gilbert
  given-names: Brian
  email: bgilbert345@gmail.com
- family-names: Datta
  given-names: Abhirup
  email: abhidatta@jhu.edu
repository: https://sandy-pramanik.r-universe.dev
repository-code: https://github.com/sandy-pramanik/vacalibration
commit: 02645051968bb26ecf9bb335ba39de9bff04a264
url: https://github.com/sandy-pramanik/vacalibration
date-released: '2026-03-20'
contact:
- family-names: Pramanik
  given-names: Sandipan
  email: sandy.pramanik@gmail.com
  orcid: https://orcid.org/0000-0002-7196-155X