vacalibration: Calibration of Computer-Coded Verbal Autopsy Algorithm
Calibrates cause-specific mortality fractions (CSMF) estimates generated by computer-coded verbal autopsy (CCVA) algorithms from WHO-standardized verbal autopsy (VA) survey data. It leverages data from the multi-country Child Health and Mortality Prevention Surveillance (CHAMPS) project <https://champshealth.org/>, which determines gold standard causes of death via Minimally Invasive Tissue Sampling (MITS). By modeling the CHAMPS data using the misclassification matrix modeling framework proposed in Pramanik et al. (2025, <doi:10.1214/24-AOAS2006>), the package includes an inventory of 48 uncertainty-quantified misclassification matrices for three CCVA algorithms (EAVA, InSilicoVA, InterVA), two age groups (neonates aged 0-27 days and children aged 1-59 months), and eight "countries" (seven countries in CHAMPS – Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, South Africa – and an estimate for countries not in CHAMPS). Given a VA-only data for an age group, CCVA algorithm, and country, the package uses the corresponding uncertainty-quantified misclassification matrix estimates as an informative prior, and utilizes the modular VA-calibration to produce calibrated CSMF estimates. It also supports ensemble calibration when VA-only data are provided for multiple algorithms. More generally, the package can be applied to calibrate predictions from a discrete classifier (or ensemble of classifiers) utilizing user-provided fixed or uncertainty-quantified misclassification matrices. This work is supported by the Bill and Melinda Gates Foundation Grant INV-034842.
| Version: |
2.0 |
| Depends: |
R (≥ 3.5) |
| Imports: |
rstan, ggplot2, loo, patchwork, reshape2 |
| Suggests: |
knitr, rmarkdown |
| Published: |
2025-07-24 |
| 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> |
| License: |
GPL-2 |
| NeedsCompilation: |
no |
| CRAN checks: |
vacalibration results |
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