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

Documentation:

Reference manual:	vacalibration.html , vacalibration.pdf
Vignettes:	Vignette for 'vacalibration' (source, R code)

Downloads:

Package source:	vacalibration_2.0.tar.gz
Windows binaries:	r-devel: not available, r-release: vacalibration_2.0.zip, r-oldrel: vacalibration_2.0.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): vacalibration_2.0.tgz, r-oldrel (x86_64): vacalibration_2.0.tgz

Linking:

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