arXiv subjects

Jamie Perin

Publications and source records attributed to Jamie Perin.

3 recordsLinked to original sources

arXiv2026

VA-Calibration: Correcting for Algorithmic Misclassification in Estimating Cause Distributions

Accurate estimation of cause-specific mortality fractions (CSMFs), the percentage of deaths attributable to each cause in a population, is essential for global health monitoring. Challenge arises because computer-coded verbal autopsy (CCVA) algorithms, commonly used to estimate CSMFs, frequently misclassify the cause of death (COD). This misclassification is further complicated by structured patterns and substantial variation across countries. To address this, we introduce the R package 'vacalibration'. It implements a modular Bayesian framework to correct for the misclassification, thereby yielding more accurate CSMF estimates from verbal autopsy (VA) questionnaire data. The package utilizes uncertainty-quantified CCVA misclassification matrix estimates derived from data collected in the CHAMPS project and available on the 'CCVA-Misclassification-Matrices' GitHub repository. Currently, these matrices cover 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. The 'vacalibration' package also supports ensemble calibration when multiple algorithms are available. Implemented using the 'RStan', the package offers rapid computation, uncertainty quantification, and seamless compatibility with openVA, a leading COD analysis software ecosystem. We demonstrate the package's flexibility with two real-world applications in COMSA-Mozambique and CA CODE. The package and its foundational methodology applies more broadly and can calibrate any discrete classifier or their ensemble.

stat.AP↗

arXiv2023

Bayesian Age Category Reconciliation for Age- and Cause-specific Under-five Mortality Estimates

Age-disaggregated health data is crucial for effective public health planning and monitoring. Monitoring under-five mortality, for example, requires highly detailed age data since the distribution of potential causes of death varies substantially within the first few years of life. Comparative researchers often have to rely on multiple data sources yet, these sources often have ages aggregated at different levels, making it difficult to combine the data into a single, coherent picture. To address this challenge in the context of under-five cause-specific mortality, we propose a Bayesian approach, that calibrates data with different age structures to produce unified and accurate estimates of the standardized age group distributions. We consider age-disaggregated death counts as fully-classified multinomial data and show that by incorporating partially-classified aggregated data, we can construct an improved Bayes estimator of the multinomial parameters under the Kullback-Leibler (KL) loss. We illustrate the method using both synthetic and real data, demonstrating that the proposed method achieves adequate performance in imputing incomplete classification. Finally, we present the results of numerical studies examining the conditions necessary for obtaining improved estimators. These studies provide insights and interpretations that can be used to aid future research and inform guidance for practitioners on appropriate levels of age disaggregation, with the aim of improving the accuracy and reliability of under-five cause-specific mortality estimates.

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arXiv2020

A flexible Bayesian framework to estimate age- and cause-specific child mortality over time from sample registration data

In order to implement disease-specific interventions in young age groups, policy makers in low- and middle-income countries require timely and accurate estimates of age- and cause-specific child mortality. High quality data is not available in settings where these interventions are most needed, but there is a push to create sample registration systems that collect detailed mortality information. Current methods that estimate mortality from this data employ multistage frameworks without rigorous statistical justification that separately estimate all-cause and cause-specific mortality and are not sufficiently adaptable to capture important features of the data. We propose a flexible Bayesian modeling framework to estimate age- and cause-specific child mortality from sample registration data. We provide a theoretical justification for the framework, explore its properties via simulation, and use it to estimate mortality trends using data from the Maternal and Child Health Surveillance System in China.

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