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vacalibration  

Calibration of Computer-Coded Verbal Autopsy Algorithm
View on CRAN: Click here


Download and install vacalibration package within the R console
Install from CRAN:
install.packages("vacalibration")

Install from Github:
library("remotes")
install_github("cran/vacalibration")

Install by package version:
library("remotes")
install_version("vacalibration", "2.0")



Attach the package and use:
library("vacalibration")
Maintained by
Sandipan Pramanik
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-07-24
Latest Update: 2025-07-24
Description:
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.
How to cite:
Sandipan Pramanik (2025). vacalibration: Calibration of Computer-Coded Verbal Autopsy Algorithm. R package version 2.0, https://cran.r-project.org/web/packages/vacalibration. Accessed 12 Jun. 2026.
Previous versions and publish date:
2.0 (2025-07-24 14:50)
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