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Accurate estimates of subnational health and demographic indicators are critical for informing health policy decisions. Many countries collect relevant data using complex household surveys, but when data are limited, direct survey weighted estimates of small area proportions may be unreliable. Area level models treating these direct estimates as response data can improve precision but often require known sampling variances of the direct estimators for all areas. In practice, the sampling variances are typically estimated, so standard approaches do not account for a key source of uncertainty. In order to account for variability in the estimated sampling variances, we propose a hierarchical Bayesian spatial area level model that smooths both the estimated means and sampling variances to produce point and interval estimates of small area proportions. Our model explicitly targets estimation of small area proportions rather than means of continuous variables and we consider examples of both moderate and low prevalence events. We demonstrate the performance of our approach via simulation and application to vaccination coverage and HIV prevalence data from the Demographic and Health Surveys.

In countries where population census data are limited, generating accurate subnational estimates of health and demographic indicators is challenging. Existing model-based geostatistical methods leverage covariate information and spatial smoothing to reduce the variability of estimates but often ignore survey design, while traditional small area estimation approaches may not incorporate both unit level covariate information and spatial smoothing in a design-consistent way. We propose a smoothed model-assisted estimator that accounts for survey design and leverages both unit level covariates and spatial smoothing. Under certain assumptions, this estimator is both design-consistent and model-consistent. We compare it with existing design-based and model-based estimators using real and simulated data., Comment: 56 pages, 6 figures

Spatial aggregation with respect to a population distribution involves estimating aggregate quantities for a population based on an observation of individuals in a subpopulation. In this context, a geostatistical workflow must account for three major sources of `aggregation error': aggregation weights, fine scale variation, and finite population variation. However, common practice is to treat the unknown population distribution as a known population density and ignore empirical variability in outcomes. We improve common practice by introducing a `sampling frame model' that allows aggregation models to account for the three sources of aggregation error simply and transparently. We compare the proposed and the traditional approach using two simulation studies that mimic neonatal mortality rate (NMR) data from the 2014 Kenya Demographic and Health Survey (KDHS2014). For the traditional approach, undercoverage/overcoverage depends arbitrarily on the aggregation grid resolution, while the new approach exhibits low sensitivity. The differences between the two aggregation approaches increase as the population of an area decreases. The differences are substantial at the second administrative level and finer, but also at the first administrative level for some population quantities. We find differences between the proposed and traditional approach are consistent with those we observe in an application to NMR data from the KDHS2014., Comment: main manuscript: 33 pages, 5 figures, 5 tables; supplemental materials: 15 pages, 2 figures, 15 tables

Despite substantial advances in global measles vaccination, measles disease burden remains high in many low- and middle-income countries. A key public health strategy for controling measles in such high-burden settings is to conduct supplementary immunization activities (SIAs) in the form of mass vaccination campaigns, in addition to delivering scheduled vaccination through routine immunization (RI) programs. To achieve balanced implementations of RI and SIAs, robust measurement of sub-national RI-specific coverage is crucial. In this paper, we develop a space-time smoothing model for estimating RI-specific coverage of the first dose of measles-containing-vaccines (MCV1) at sub-national level using complex survey data. The application that motivated this work is estimation of the RI-specific MCV1 coverage in Nigeria's 36 states and the Federal Capital Territory. Data come from four Demographic and Health Surveys, three Multiple Indicator Cluster Surveys, and two National Nutrition and Health Surveys conducted in Nigeria between 2003 and 2018. Our method incorporates information from the SIA calendar published by the World Health Organization and accounts for the impact of SIAs on the overall MCV1 coverage, as measured by cross-sectional surveys. The model can be used to analyze data from multiple surveys with different data collection schemes and construct coverage estimates with uncertainty that reflects the various sampling designs. Implementation of our method can be done efficiently using integrated nested Laplace approximation (INLA)., Comment: 19 pages, 10 figures

Small area estimates of population are necessary for many epidemiological studies, yet their quality and accuracy are often not assessed. In the United States, small area estimates of population counts are published by the United States Census Bureau (USCB) in the form of the Decennial census counts, Intercensal population projections (PEP), and American Community Survey (ACS) estimates. Although there are significant relationships between these data sources, there are important contrasts in data collection and processing methodologies, such that each set of estimates may be subject to different sources and magnitudes of error. Additionally, these data sources do not report identical small area population counts due to post-survey adjustments specific to each data source. Resulting small area disease/mortality rates may differ depending on which data source is used for population counts (denominator data). To accurately capture annual small area population counts, and associated uncertainties, we present a Bayesian population model (B-Pop), which fuses information from all three USCB sources, accounting for data source specific methodologies and associated errors. The main features of our framework are: 1) a single model integrating multiple data sources, 2) accounting for data source specific data generating mechanisms, and specifically accounting for data source specific errors, and 3) prediction of estimates for years without USCB reported data. We focus our study on the 159 counties of Georgia, and produce estimates for years 2005-2021.

The emerging need for subnational estimation of demographic and health indicators in low- and middle-income countries (LMICs) is driving a move from design-based area-level approaches to unit-level methods. The latter are model-based and overcome data sparsity by borrowing strength across covariates and space and can, in principle, be leveraged to create fine-scale pixel level maps based on household surveys. However, typical implementations of the model-based approaches do not fully acknowledge the complex survey design, and do not enjoy the theoretical consistency of design-based approaches. We describe how spatial methods are currently used for prevalence mapping in the context of LMICs, highlight the key challenges that need to be overcome, and propose a new approach, which is methodologically closer in spirit to small area estimation. The main discussion points are demonstrated through a case study of vaccination coverage in Nigeria based on 2018 Demographic and Health Surveys (DHS) data. We discuss our key findings both generally and with an emphasis on the implications for popular approaches undertaken by industrial producers of subnational prevalence estimates., Comment: An extensive revision of the previous version of the preprint. The spatial aspects have been fleshed out more, and the temporal aspects have been removed

The integrated nested Laplace approximation (INLA) is a well-known and popular technique for spatial modeling with a user-friendly interface in the R-INLA package. Unfortunately, only a certain class of latent Gaussian models are amenable to fitting with INLA. In this paper we describe Template Model Builder (TMB), an existing technique which is well-suited to fitting complex spatio-temporal models. TMB is relatively unknown to the spatial statistics community, but is a highly flexible random effects modeling tool which allows users to define complex random effects models through simple C++ templates. After contrasting the methodology behind TMB with INLA, we provide a large-scale simulation study assessing and comparing R-INLA and TMB for continuous spatial models, fitted via the Stochastic Partial Differential Equations (SPDE) approximation. The results show that the predictive fields from both methods are comparable in most situations even though TMB estimates for fixed or random effects may have slightly larger bias than R-INLA. We also present a smaller discrete spatial simulation study, in which both approaches perform well. We conclude with an analysis of breast cancer incidence and mortality data using a joint model which cannot be fit with INLA., Comment: 84 pages, 30 figures

Small area estimation (SAE) entails estimating characteristics of interest for domains, often geographical areas, in which there may be few or no samples available. SAE has a long history and a wide variety of methods have been suggested, from a bewildering range of philosophical standpoints. We describe design-based and model-based approaches and models that are specified at the area-level and at the unit-level, focusing on health applications and fully Bayesian spatial models. The use of auxiliary information is a key ingredient for successful inference when response data are sparse and we discuss a number of approaches that allow the inclusion of covariate data. SAE for HIV prevalence, using data collected from a Demographic Health Survey in Malawi in 2015-2016, is used to illustrate a number of techniques. The potential use of SAE techniques for outcomes related to COVID-19 is discussed., Comment: 53 pages, 27 figures

Current implementations of multiresolution methods are limited in terms of possible types of responses and approaches to inference. We provide a multiresolution approach for spatial analysis of non-Gaussian responses using latent Gaussian models and Bayesian inference via integrated nested Laplace approximation (INLA). The approach builds on `LatticeKrig', but uses a reparameterization of the model parameters that is intuitive and interpretable so that modeling and prior selection can be guided by expert knowledge about the different spatial scales at which dependence acts. The priors can be used to make inference robust and integration over model parameters allows for more accurate posterior estimates of uncertainty. The extended LatticeKrig (ELK) model is compared to a standard implementation of LatticeKrig (LK), and a standard Mat\'ern model, and we find modest improvement in spatial oversmoothing and prediction for the ELK model for counts of secondary education completion for women in Kenya collected in the 2014 Kenya demographic health survey. Through a simulation study with Gaussian responses and a realistic mix of short and long scale dependencies, we demonstrate that the differences between the three approaches for prediction increases with distance to nearest observation., Comment: main manuscript: 33 pages, 7 figures, 2 tables; supplemental materials: 9 pages, 3 figures, 5 tables

BACKGROUND There is an increasing demand for high quality subnational estimates of under-five mortality. In low and middle income countries, where the burden of under-five mortality is concentrated, vital registration is often lacking and household surveys, which provide full birth history data, are often the most reliable source. Unfortunately, these data are spatially sparse and so data are pulled from other sources to increase the available information. Summary birth histories represent a large fraction of the available data, and provide numbers of births and deaths aggregated over time, along with the mother's age. OBJECTIVE Specialized methods are needed to leverage this information, and previously the Brass method, and variants, have been used. We wish to develop a model-based approach that can propagate errors, and make the most efficient use of the data. Further, we strive to provide a method that does not have large computational overhead. CONTRIBUTION We describe a computationally efficient model-based approach which allows summary birth history and full birth history data to be combined into analyses of under-five mortality in a natural way. The method is based on fertility and mortality models that allow direct smoothing over time and space, with the possibility for including relevant covariates that are associated with fertility and/or mortality. We first examine the behavior of the approach on simulated data, before applying the model to survey and census data from Malawi.

The need for rigorous and timely health and demographic summaries has provided the impetus for an explosion in geographic studies, with a common approach being the production of pixel-level maps, particularly in low and middle income countries. In this context, household surveys are a major source of data, usually with a two-stage cluster design with stratification by region and urbanicity. Accurate estimates are of crucial interest for precision public health policy interventions, but many current studies take a cavalier approach to acknowledging the sampling design, while presenting results at a fine geographic scale. In this paper we investigate the extent to which accounting for sample design can affect predictions at the aggregate level, which is usually the target of inference. We describe a simulation study in which realistic sampling frames are created for Kenya, based on population and demographic information, with a survey design that mimics a Demographic Health Survey (DHS). We compare the predictive performance of various commonly-used models. We also describe a cluster level model with a discrete spatial smoothing prior that has not been previously used, but provides reliable inference. We find that including stratification and cluster level random effects can improve predictive performance. Spatially smoothed direct (weighted) estimates were robust to priors and survey design. Continuous spatial models performed well in the presence of fine scale variation; however, these models require the most "hand holding". Subsequently, we examine how the models perform on real data; specifically we model the prevalence of secondary education for women aged 20-29 using data from the 2014 Kenya DHS., Comment: Main text: 35 pages, 5 figures, 2 tables. Supplementary materials: 63 pages, 5 figures, 21 tables

Methods (DOCX 14Â kb)

Seasonal incidence of methicillin-resistant Staphylococcus aureus, Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Haemophilus influenzae acquisition among children

Traditionally health statistics are derived from civil and/or vital registration. Civil registration in low-income countries varies from partial coverage to essentially nothing at all. Consequently the state of the art for public health information in low-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: 1) Data Amalgamation: a sampling and surveillance component that organizes two or more data collection systems to work together: a) data from HDSS with frequent, intense, linked, prospective follow-up and b) data from sample surveys conducted in large areas surrounding the Health and Demographic Surveillance System sites using informed sampling so as to capture as many events as possible; 2) Cause of Death: verbal autopsy to characterize the distribution of deaths by cause at the population level; and 3) SES: measurement of socioeconomic status 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 to traditional cluster sampling, Hyak's informed sampling captures more deaths, and when combined with an estimation model that includes spatial smoothing, produces estimates mortality that have lower variance and small bias., Comment: Updated version including new simulation study with two-stage cluster and optimum allocation sampling

Verbal autopsies (VA) are widely used to provide cause-specific mortality estimates in developing world settings where vital registration does not function well. VAs assign cause(s) to a death by using information describing the events leading up to the death, provided by care givers. Typically physicians read VA interviews and assign causes using their expert knowledge. Physician coding is often slow, and individual physicians bring bias to the coding process that results in non-comparable cause assignments. These problems significantly limit the utility of physician-coded VAs. A solution to both is to use an algorithmic approach that formalizes the cause-assignment process. This ensures that assigned causes are comparable and requires many fewer person-hours so that cause assignment can be conducted quickly without disrupting the normal work of physicians. Peter Byass' InterVA method is the most widely used algorithmic approach to VA coding and is aligned with the WHO 2012 standard VA questionnaire. The statistical model underpinning InterVA can be improved; uncertainty needs to be quantified, and the link between the population-level CSMFs and the individual-level cause assignments needs to be statistically rigorous. Addressing these theoretical concerns provides an opportunity to create new software using modern languages that can run on multiple platforms and will be widely shared. Building on the overall framework pioneered by InterVA, our work creates a statistical model for automated VA cause assignment., Comment: 20 pages, 4 figures, Center for Statistics and the Social Sciences (CSSS), University of Washington Working Paper No. 133

Supplemental material for Estimating under-five mortality in space and time in a developing world context by Jon Wakefield, Geir-Arne Fuglstad, Andrea Riebler, Jessica Godwin, Katie Wilson and Samuel J Clark in Statistical Methods in Medical Research

Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2-to end preventable child deaths by 2030-we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000-2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations.

Stochastic epidemic models describe the dynamics of an epidemic as a disease spreads through a population. Typically, only a fraction of cases are observed at a set of discrete times. The absence of complete information about the time evolution of an epidemic gives rise to a complicated latent variable problem in which the state space size of the epidemic grows large as the population size increases. This makes analytically integrating over the missing data infeasible for populations of even moderate size. We present a data augmentation Markov chain Monte Carlo (MCMC) framework for Bayesian estimation of stochastic epidemic model parameters, in which measurements are augmented with subject-level disease histories. In our MCMC algorithm, we propose each new subject-level path, conditional on the data, using a time-inhomogenous continuous-time Markov process with rates determined by the infection histories of other individuals. The method is general, and may be applied to a broad class of epidemic models with only minimal modifications to the model dynamics and/or emission distribution. We present our algorithm in the context of multiple stochastic epidemic models in which the data are binomially sampled prevalence counts, and apply our method to data from an outbreak of influenza in a British boarding school. Supplementary material for this article is available online.

Stochastic epidemic models describe the dynamics of an epidemic as a disease spreads through a population. Typically, only a fraction of cases are observed at a set of discrete times. The absence of complete information about the time evolution of an epidemic gives rise to a complicated latent variable problem in which the state space size of the epidemic grows large as the population size increases. This makes analytically integrating over the missing data infeasible for populations of even moderate size. We present a data augmentation Markov chain Monte Carlo (MCMC) framework for Bayesian estimation of stochastic epidemic model parameters, in which measurements are augmented with subject-level disease histories. In our MCMC algorithm, we propose each new subject-level path, conditional on the data, using a time-inhomogenous continuous-time Markov process with rates determined by the infection histories of other individuals. The method is general, and may be applied to a broad class of epidemic models with only minimal modifications to the model dynamics and/or emission distribution. We present our algorithm in the context of multiple stochastic epidemic models in which the data are binomially sampled prevalence counts, and apply our method to data from an outbreak of influenza in a British boarding school. Supplementary material for this article is available online.