Li Zehang Richard, Thomas Jason, Choi Eungang, McCormick Tyler H, Clark Samuel J
University of California, Santa Cruz, Santa Cruz CA, USA.
The Ohio State University, Columbus, OH, USA.
R J. 2022 Dec;14(4):316-334. doi: 10.32614/rj-2023-020. Epub 2023 Feb 24.
Verbal autopsy (VA) is a survey-based tool widely used to infer cause of death (COD) in regions without complete-coverage civil registration and vital statistics systems. In such settings, many deaths happen outside of medical facilities and are not officially documented by a medical professional. VA surveys, consisting of signs and symptoms reported by a person close to the decedent, are used to infer the COD for an individual, and to estimate and monitor the COD distribution in the population. Several classification algorithms have been developed and widely used to assign causes of death using VA data. However, the incompatibility between different idiosyncratic model implementations and required data structure makes it difficult to systematically apply and compare different methods. The openVA package provides the first standardized framework for analyzing VA data that is compatible with all openly available methods and data structure. It provides an open-source, R implementation of several most widely used VA methods. It supports different data input and output formats, and customizable information about the associations between causes and symptoms. The paper discusses the relevant algorithms, their implementations in R packages under the openVA suite, and demonstrates the pipeline of model fitting, summary, comparison, and visualization in the R environment.
口头尸检（VA）是一种基于调查的工具，广泛用于在没有全面覆盖的民事登记和人口动态统计系统的地区推断死因（COD）。在这种情况下，许多死亡发生在医疗机构之外，并且没有医学专业人员的正式记录。VA调查由死者近亲报告的体征和症状组成，用于推断个体的死因，并估计和监测人群中的死因分布。已经开发并广泛使用了几种分类算法，用于使用VA数据确定死因。然而，不同的特殊模型实现与所需的数据结构之间的不兼容性使得难以系统地应用和比较不同的方法。openVA软件包提供了第一个用于分析VA数据的标准化框架，该框架与所有公开可用的方法和数据结构兼容。它提供了几种最广泛使用的VA方法的开源R实现。它支持不同的数据输入和输出格式，以及关于死因与症状之间关联的可定制信息。本文讨论了相关算法、它们在openVA套件下的R包中的实现，并展示了R环境中的模型拟合、汇总、比较和可视化流程。
