README

Given VA-only data for an age group, algorithm, and country, the package calibrates population-level cause-specific mortality fractions (CSMFs) produced by computer-coded verbal autopsy (CCVA) algorithms on WHO-standardized verbal autopsy (VA) surveys. It also supports ensemble calibration to accommodate multiple algorithms.

The package stores an inventory of uncertainty-quantified CCVA misclassification matrices that are obtained using the framework of Pramanik et al. (2025) based on data collected in the CHAMPS project. The inventory of 48 matrices covers three CCVA algorithms (EAVA, InSilicoVA, InterVA), two age groups (neonates 0-27 days; children 1-59 months), and eight countries (Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, South Africa, plus an “other” for all other countries). See Pramanik et al. (2025+) for analysis details.

More generally, this calibrates population-level prevalence derived from single-class predictions of discrete classifiers. Users can provide fixed or uncertainty-quantified misclassification matrices.

Credit

Funding Acknowledgement

Bill and Melinda Gates Foundation Grant (INV-034842); Johns Hopkins Data Science and AI Institute; Eunice Kennedy Shriver National Institute of Child Health K99 NIH Pathway to Independence Award (1K99HD114884-01A1).

Installation

install.packages("vacalibration") # install
library(vacalibration) # load

Example

In the following example, we demonstrate how vacalibration() can be used to perform algorithm-specific and ensemble calibrations, and generate calibrated CSMF estimates. For brevity, we exclude the diagnostic and summary plots as well as the detailed output of the posterior sampling.

Algorithm-Specific Calibration

vacalib_eava = vacalibration(va_data = list("eava" = comsamoz_CCVAoutput$neonate$eava), 
                             age_group = "neonate", country = "Mozambique")

# CSMF
vacalib_eava$p_uncalib[1,]  # uncalibrated estimates
vacalib_eava$p_calib[1,,]  # posterior of calibrated estimates
vacalib_eava$pcalib_postsumm[1,,]  # posterior summary of calibrated estimates

# death counts
vacalib_eava$va_deaths_uncalib[1,]  # uncalibrated
vacalib_eava$va_deaths_calib_algo[1,]  # calibrated

InSilicoVA and InterVA-specific VA-calibration can be similarly performed by replacing va_data = list("insilicova" = comsamoz_CCVAoutput$neonate$insilicova) and va_data = list("interva" = comsamoz_CCVAoutput$neonate$interva).

Use missmat_type to control uncertainty propagation. missmat_type = "fixed" calibrates using a fixed misclassification matrix (by default, the average matrix in CCVA_missmat) and does not propagate uncertainty. missmat_type = "prior" (package default) or missmat_type = "samples" propagates uncertainty and is recommended.

To calibrate with posterior samples, use missmat_type = "samples" and missmat = CCVA_missmat$neonate$eava$postsamples$Mozambique in the example. Note: CCVA_missmat included in the package does not contain posterior samples due to file size limits. If needed, obtain them from the CCVA_missmat object in the GitHub repository and pass them to vacalibration().

Ensemble Calibration

To perform ensemble calibration, provide a list algorithm-specific CCVA outputs. This performs both algorithm-specific calibration and an ensemble calibration. Set ensemble = FALSE to turn off ensemble calibration.

vacalib_ensemble = 
  vacalibration(va_data = list("eava" = comsamoz_CCVAoutput$neonate$eava,
                               "insilicova" = comsamoz_CCVAoutput$neonate$insilicova,
                               "interva" = comsamoz_CCVAoutput$neonate$interva),
                age_group = "neonate", country = "Mozambique")

# CSMF
vacalib_ensemble$p_uncalib  # uncalibrated estimates

# posterior of calibrated CSMF
vacalib_ensemble$p_calib["eava",,]  # EAVA
vacalib_ensemble$p_calib["insilicova",,]  # InSilicoVA
vacalib_ensemble$p_calib["interva",,]  # InterVA
vacalib_ensemble$p_calib["ensemble",,]  # ensemble

# posterior summary of calibrated CSMF
vacalib_ensemble$pcalib_postsumm["eava",,]  # EAVA
vacalib_ensemble$pcalib_postsumm["insilicova",,]  # InSilicoVA
vacalib_ensemble$pcalib_postsumm["interva",,]  # InterVA
vacalib_ensemble$pcalib_postsumm["ensemble",,]  # ensemble

# death counts
vacalib_ensemble$va_deaths_uncalib  # uncalibrated
vacalib_ensemble$va_deaths_calib_algo  # calibrated counts based on algorithm-specific calibration
vacalib_ensemble$va_deaths_calib_ensemble  # calibrated counts based on ensemble calibration

If missmat includes user-specified matrices, then age_group and country are not required.

Calibration for Causes Outside CHAMPS Broad Causes

As discussed in CCVA Misclassification Matrices, the matrices in CCVA_missmat are available for CHAMPS broad causes. In cases where the causes in va_data are not a subset of the CHAMPS broad causes, a cause-mapping step is required. One such application is the CA CODE project, which compiles VA-based death counts across multiple countries. For example, a study in Bangladesh analyzed 302 neonatal deaths using EAVA, and reported 82 deaths due to Intrapartum, 17 due to Congenital, 6 due to Diarrhoeal, 33 due to LRI, 108 due to Sepsis, 35 due to Preterm, 14 due to Tetanus, and 7 due to Other.

In such cases, vacalibration() requires specifying studycause_map, a mapping from the study causes to the CHAMPS broad causes. For this example, following expert guidance, we define:

set_studycause_map = c("Intrapartum" = "ipre", "Congenital" = "congenital_malformation",
                       "Diarrhoeal" = "sepsis_meningitis_inf", "LRI" = "pneumonia",
                       "Sepsis" = "sepsis_meningitis_inf", "Preterm" = "prematurity", 
                       "Tetanus" = "sepsis_meningitis_inf", "Other" = "other")

This mapping converts the misclassification matrices in CCVA_missmat to align with the study causes, enabling VA-calibration. This can then be implemented as:



vacalib_cacode = vacalibration(va_data = list("eava" = c("Intrapartum" = 82, "Congenital" = 17,
                                                         "Diarrhoeal" = 6, "LRI" = 33,
                                                         "Sepsis" = 108, "Preterm" = 35, 
                                                         "Tetanus" = 14, "Other" = 7)), 
                               age_group = "neonate", country = "Bangladesh",
                               studycause_map = set_studycause_map)

# CSMF
vacalib_cacode$p_uncalib[1,]  # uncalibrated estimates
vacalib_cacode$p_calib[1,,]  # posterior of calibrated estimates
vacalib_cacode$pcalib_postsumm[1,,]  # posterior summary of calibrated estimates

# death counts
vacalib_cacode$va_deaths_uncalib[1,]  # uncalibrated
vacalib_cacode$va_deaths_calib_algo[1,]  # calibrated

This is required only when using the misclassification matrices from CCVA_missmat. If missmat includes user-specified matrices, then age_group, country, and studycause_map are not required.