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Background A verbal autopsy (VA) is an interview conducted with the caregivers of someone who has recently died to describe the circumstances of the death. In recent years, several algorithmic methods have been developed to classify cause of death using VA data. The performance of one method—InSilicoVA—was evaluated in a study by Flaxman et al., published in BMC Medicine in 2018. The results of that study are different from those previously published by our group. Methods Based on the description of methods in the Flaxman et al. study, we attempt to replicate the analysis to understand why the published results differ from those of our previous work. Results We failed to reproduce the results published in Flaxman et al. Most of the discrepancies we find likely result from undocumented differences in data pre-processing, and/or values assigned to key parameters governing the behavior of the algorithm. Conclusion This finding highlights the importance of making replication code available along with published results. All code necessary to replicate the work described here is freely available on GitHub.

The under-five mortality rate (U5MR) is a critical and widely available population health indicator. Both the MDGs and SDGs define targets for improvement in the U5MR, and the SDGs require spatial disaggregation of indicators. We estimate trends in the U5MR for Admin-1 subnational areas using 122 DHS surveys in 35 countries in Africa and assess progress toward the MDG target reductions for each subnational region and each country as a whole. In each country, direct weighted estimates of the U5MR from each survey are calculated and combined into a single estimate for each Admin-1 region across five-year periods. Our method fully accounts for the sample design of each survey. The region-time-specific estimates are smoothed using a Bayesian, space-time model that produces more precise estimates (when compared to the direct estimates) at a one-year scale that are consistent with each other in both space and time. The resulting estimated distributions of the U5MR are summarized and used to assess subnational progress toward the MDG 4 target of two-thirds reduction in the U5MR during 1990-2015. Our space-time modeling approach is tractable and can be readily applied to a large collection of sample survey data. Subnational, regional spatial heterogeneity in the levels and trends in the U5MR vary considerably across Africa. There is no generalizable pattern between spatial heterogeneity and levels or trends in the U5MR. Subnational, small-area estimates of the U5MR: (i) identify subnational regions where interventions are still necessary and those where improvement is well under way; and (ii) countries where there is very little spatial variation and others where there are important differences between subregions in both levels and trends. More work is necessary to improve both the data sources and methods necessary to adequately measure subnational progress toward the SDG child survival targets.

The distribution of deaths by cause provides crucial information for public health planning, response, and evaluation. About 60% of deaths globally are not registered or given a cause, limiting our ability to understand disease epidemiology. Verbal autopsy (VA) surveys are increasingly used in such settings to collect information on the signs, symptoms, and medical history of people who have recently died. This article develops a novel Bayesian method for estimation of population distributions of deaths by cause using verbal autopsy data. The proposed approach is based on a multivariate probit model where associations among items in questionnaires are flexibly induced by latent factors. Using the Population Health Metrics Research Consortium labeled data that include both VA and medically certified causes of death, we assess performance of the proposed method. Further, we estimate important questionnaire items that are highly associated with causes of death. This framework provides insights that will simplify future data collection.

We show that Bayesian population reconstruction, a recent method for estimating past populations by age, works for data of widely varying quality. Bayesian reconstruction simultaneously estimates age-specific population counts, fertility rates, mortality rates, and net international migration flows from fragmentary data, while formally accounting for measurement error. As inputs, Bayesian reconstruction uses initial bias-reduced estimates of standard demographic variables. We reconstruct the female populations of three countries: Laos, a country with little vital registration data where population estimation depends largely on surveys; Sri Lanka, a country with some vital registration data; and New Zealand, a country with a highly developed statistical system and good quality vital registration data. In addition, we extend the method to countries without censuses at regular intervals. We also use it to assess the consistency of results between model life tables and available census data, and hence to compare different model life table systems.

Traditionally health statistics are derived from civil and/or vital registration. Civil registration in low- to middle-income countries varies from partial coverage to essentially nothing at all. Consequently the state of the art for public health information in low- to middle-income countries is efforts to combine or triangulate data from different sources to produce a more complete picture across both time and space – data amalgamation. Data sources amenable to this approach include sample surveys, sample registration systems, health and demographic surveillance systems, administrative records, census records, health facility records and others. We propose a new statistical framework for gathering health and population data – Hyak – that leverages the benefits of sampling and longitudinal, prospective surveillance to create a cheap, accurate, sustainable monitoring platform. Hyak has three fundamental components: •Data amalgamation: A sampling and surveillance component that organizes two or more data collection systems to work together: (1) data from HDSS with frequent, intense, linked, prospective follow-up and (2) data from sample surveys conducted in large areas surrounding the Health and Demographic Surveillance System (HDSS) sites using informed sampling so as to capture as many events as possible;•Cause of death: Verbal autopsy to characterize the distribution of deaths by cause at the population level; and•Socioeconomic status (SES): Measurement of SES in order to characterize poverty and wealth.We conduct a simulation study of the informed sampling component of Hyak based on the Agincourt HDSS site in South Africa. Compared with traditional cluster sampling, Hyak's informed sampling captures more deaths, and when combined with an estimation model that includes spatial smoothing, produces estimates of both mortality counts and mortality rates that have lower variance and small bias.

Accurate estimates of the under-5 mortality rate (U5MR) in a developing world context are a key barometer of the health of a nation. This paper describes new models to analyze survey data on mortality in this context. We are interested in both spatial and temporal description, that is, wishing to estimate U5MR across regions and years, and to investigate the association between the U5MR and spatially-varying covariate surfaces. We illustrate the methodology by producing yearly estimates for subnational areas in Kenya over the period 1980 - 2014 using data from demographic health surveys (DHS). We use a binomial likelihood with fixed effects for the urban/rural stratification to account for the complex survey design. We carry out smoothing using Bayesian hierarchical models with continuous spatial and temporally discrete components. A key component of the model is an offset to adjust for bias due to the effects of HIV epidemics. Substantively, there has been a sharp decline in U5MR in the period 1980 - 2014, but large variability in estimated subnational rates remains. A priority for future research is understanding this variability. Temperature, precipitation and a measure of malaria infection prevalence were candidates for inclusion in the covariate model., 36 pages, 11 figures

In regions without complete-coverage civil registration and vital statistics systems there is uncertainty about even the most basic demographic indicators. In such regions the majority of deaths occur outside hospitals and are not recorded. Worldwide, fewer than one-third of deaths are assigned a cause, with the least information available from the most impoverished nations. In populations like this, verbal autopsy (VA) is a commonly used tool to assess cause of death and estimate cause-specific mortality rates and the distribution of deaths by cause. VA uses an interview with caregivers of the decedent to elicit data describing the signs and symptoms leading up to the death. This paper develops a new statistical tool known as InSilicoVA to classify cause of death using information acquired through VA. InSilicoVA shares uncertainty between cause of death assignments for specific individuals and the distribution of deaths by cause across the population. Using side-by-side comparisons with both observed and simulated data, we demonstrate that InSilicoVA has distinct advantages compared to currently available methods.

BACKGROUND Estimating the total fertility rate is challenging for many developing countries because of limited data and varying data quality. A standardized, reproducible approach to produce estimates that include an uncertainty assessment is desired. METHODS We develop a method to estimate and assess uncertainty in the total fertility rate over time, based on multiple imperfect observations from different data sources including surveys and censuses. We take account of measurement error in observations by decomposing it into bias and variance and assess both by linear regression on a variety of data quality covariates. We estimate the total fertility rate using a local smoother, and assess uncertainty using the weighted likelihood bootstrap. RESULTS We apply our method to data from seven countries in West Africa and construct estimates and uncertainty intervals for the total fertility rate. Based on cross-validation exercises, we find that accounting for differences in data quality between observations gives better calibrated confidence intervals and reduces bias. CONCLUSIONS When working with multiple imperfect observations from different data sources to estimate the total fertility rate, or demographic indicators in general, potential biases and differences in error variance have to be taken into account to improve the estimates and their uncertainty assessment.

BACKGROUND Much of our knowledge of the epidemiology and demography of HIV epidemics in Africais derived from models fit to sparse, non-representative data. These often average over ageand other important dimensions, rarely quantify uncertainty, and typically do not imposeconsistency on the epidemiology and the demography of the population. OBJECTIVE This work conducts an empirical investigation of the history of the HIV epidemic inUganda and Tanzania through the late 1990s, focusing on sex-age-specific incidence,uses those results to produce probabilistic forecasts of HIV prevalence ten years later,and compares those to measures of HIV prevalence at the later time to describe the sexagepattern of changes in prevalence over the intervening period. METHODS We adapt an epidemographic model of a population affected by HIV so that its parameterscan be estimated using both the Bayesian melding with IMIS estimation methodand maximum likelihood methods. Using the Bayesian version of the model we produceprobabilistic forecasts of the population with HIV. RESULTS We produce estimates of sex-age-specific HIV incidence in Uganda and Tanzania in thelate 1990s, produce probabilistic forecasts of the HIV epidemics in Uganda and Tanzaniaduring the early 2000s, describe the sex-age pattern of changes in HIV prevalence inUganda during the early 2000s, and compare the performance and results of the Bayesianand maximum likelihood estimation procedures. CONCLUSIONS We demonstrate that: (1) it is possible to model HIV epidemics in Africa taking accountof sex and age, (2) there are important advantages to the Bayesian estimation method,including rigorous quantification of uncertainty and the ability to make probabilistic forecasts,and (3) that there were important age-specific changes in HIV incidence in Ugandaduring the early 2000s.

The United Nations (UN) issued official probabilistic population projections for all countries to 2100 in July 2015. This was done by simulating future levels of total fertility and life expectancy from Bayesian hierarchical models, and combining the results using a standard cohort-component projection method. The 40 countries with generalized HIV/AIDS epidemics were treated differently from others, in that the projections used the highly multistate Spectrum/EPP model, a complex 15-compartment model that was designed for short-term projections of quantities relevant to policy for the epidemic. Here we propose a simpler approach that is more compatible with the existing UN probabilistic projection methodology for other countries. Changes in life expectancy are projected probabilistically using a simple time series regression model on current life expectancy, HIV prevalence and ART coverage. These are then converted to age- and sex-specific mortality rates using a new family of model life tables designed for countries with HIV/AIDS epidemics that reproduces the characteristic hump in middle adult mortality. These are then input to the standard cohort-component method, as for other countries. The method performed well in an out-of-sample cross-validation experiment. It gives similar population projections to Spectrum/EPP in the short run, while being simpler and avoiding multistate modeling.

The Agincourt Health and Demographic Surveillance System has since 2001 conducted a biannual household asset survey in order to quantify household socio-economic status (SES) in a rural population living in northeast South Africa. The survey contains binary, ordinal and nominal items. In the absence of income or expenditure data, the SES landscape in the study population is explored and described by clustering the households into homogeneous groups based on their asset status. A model-based approach to clustering the Agincourt households, based on latent variable models, is proposed. In the case of modeling binary or ordinal items, item response theory models are employed. For nominal survey items, a factor analysis model, similar in nature to a multinomial probit model, is used. Both model types have an underlying latent variable structure - this similarity is exploited and the models are combined to produce a hybrid model capable of handling mixed data types. Further, a mixture of the hybrid models is considered to provide clustering capabilities within the context of mixed binary, ordinal and nominal response data. The proposed model is termed a mixture of factor analyzers for mixed data (MFA-MD). The MFA-MD model is applied to the survey data to cluster the Agincourt households into homogeneous groups. The model is estimated within the Bayesian paradigm, using a Markov chain Monte Carlo algorithm. Intuitive groupings result, providing insight to the different socio-economic strata within the Agincourt region., Comment: Published in at http://dx.doi.org/10.1214/14-AOAS726 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)

Current methods for reconstructing human populations of the past by age and sex are deterministic or do not formally account for measurement error. We propose a method for simultaneously estimating age-specific population counts, fertility rates, mortality rates, and net international migration flows from fragmentary data that incorporates measurement error. Inference is based on joint posterior probability distributions that yield fully probabilistic interval estimates. It is designed for the kind of data commonly collected in modern demographic surveys and censuses. Population dynamics over the period of reconstruction are modeled by embedding formal demographic accounting relationships in a Bayesian hierarchical model. Informative priors are specified for vital rates, migration rates, population counts at baseline, and their respective measurement error variances. We investigate calibration of central posterior marginal probability intervals by simulation and demonstrate the method by reconstructing the female population of Burkina Faso from 1960 to 2005. Supplementary materials for this article are available online and the method is implemented in the R package “popReconstruct.”