vacalibration: Calibration of Computer-Coded Verbal Autopsy Algorithm
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;<doi:10.1214/24-AOAS2006>) and are analyzed in Pramanik et al. (2026;<doi: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;<doi: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.
| Version: |
2.2 |
| Depends: |
R (≥ 3.5) |
| Imports: |
rstan, openVA, parallel, ggplot2, patchwork, reshape2, LaplacesDemon, MASS |
| Suggests: |
knitr, rmarkdown |
| Published: |
2026-03-20 |
| DOI: |
10.32614/CRAN.package.vacalibration |
| Author: |
Sandipan Pramanik 
[aut, cre],
Emily Wilson [aut],
Jacob Fiksel [aut],
Brian Gilbert [aut],
Abhirup Datta [aut] |
| Maintainer: |
Sandipan Pramanik <sandy.pramanik at gmail.com> |
| BugReports: |
https://github.com/sandy-pramanik/vacalibration/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/sandy-pramanik/vacalibration |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
vacalibration results |
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