Space-Time Smoothing of Demographic and Health Indicators using the R Package SUMMER

The increasing availability of complex survey data, and the continued need for estimates of demographic and health indicators at a fine spatial and temporal scale, which leads to issues of data sparsity, has led to the need for spatio-temporal smoothing methods that acknowledge the manner in which the data were collected. The open source R package SUMMER implements a variety of methods for spatial or spatio-temporal smoothing of survey data. The emphasis is on small-area estimation. We focus primarily on indicators in a low and middle-income countries context. Our methods are particularly useful for data from Demographic Health Surveys and Multiple Indicator Cluster Surveys. We build upon functions within the survey package, and use INLA for fast Bayesian computation. This paper includes a brief overview of these methods and illustrates the workflow of accessing and processing surveys, estimating subnational child mortality rates, and visualizing results with both simulated data and DHS surveys.

[1]  Jon Wakefield,et al.  Modeling and presentation of vaccination coverage estimates using data from household surveys. , 2020, Vaccine.

[2]  Thiago G. Martins,et al.  Penalising Model Component Complexity: A Principled, Practical Approach to Constructing Priors , 2014, 1403.4630.

[3]  Jon Wakefield,et al.  Small Area Estimation of Health Outcomes , 2020, 2006.10266.

[4]  Fengmin Zhao,et al.  Child Mortality Estimation: Methods Used to Adjust for Bias due to AIDS in Estimating Trends in Under-Five Mortality , 2012, PLoS medicine.

[5]  H. Rue,et al.  Scaling intrinsic Gaussian Markov random field priors in spatial modelling , 2014 .

[6]  J. Besag,et al.  Bayesian image restoration, with two applications in spatial statistics , 1991 .

[7]  Jun Yan Gaussian Markov Random Fields: Theory and Applications. Harvard Rue and Leonhard Held , 2006 .

[8]  Kenneth Hill,et al.  Demographic estimation: a manual on indirect techniques. , 1981 .

[9]  Jon Wakefield,et al.  Changes in the spatial distribution of the under-five mortality rate: Small-area analysis of 122 DHS surveys in 262 subregions of 35 countries in Africa , 2019, PloS one.

[10]  John Bryant,et al.  Fully Bayesian Benchmarking of Small Area Estimation Models , 2020 .

[11]  Rachel M. Harter,et al.  An Error-Components Model for Prediction of County Crop Areas Using Survey and Satellite Data , 1988 .

[12]  S. Martino Approximate Bayesian Inference for Latent Gaussian Models , 2007 .

[13]  Thomas Lumley,et al.  Analysis of Complex Survey Samples , 2004 .

[14]  D. Horvitz,et al.  A Generalization of Sampling Without Replacement from a Finite Universe , 1952 .

[15]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[16]  Jon Pedersen,et al.  Child Mortality Estimation: Appropriate Time Periods for Child Mortality Estimates from Full Birth Histories , 2012, PLoS medicine.

[17]  Yolanda Marhuenda,et al.  sae: An R Package for Small Area Estimation , 2015, R J..

[18]  Andrea Riebler,et al.  An intuitive Bayesian spatial model for disease mapping that accounts for scaling , 2016, Statistical methods in medical research.

[19]  Haavard Rue,et al.  Penalised Complexity Priors for Stationary Autoregressive Processes , 2016, 1608.08941.

[20]  D. Basu,et al.  An Essay on the Logical Foundations of Survey Sampling, Part One* , 2011 .

[21]  Jin Rou New,et al.  Global estimation of child mortality using a Bayesian B-spline Bias-reduction model , 2013, 1309.1602.

[22]  Jon Wakefield,et al.  Estimating under-five mortality in space and time in a developing world context , 2017, Statistical methods in medical research.

[23]  Lynne Stokes Introduction to Variance Estimation , 2008 .

[24]  R. Fay,et al.  Estimates of Income for Small Places: An Application of James-Stein Procedures to Census Data , 1979 .

[25]  L Knorr-Held,et al.  Bayesian modelling of inseparable space-time variation in disease risk. , 2000, Statistics in medicine.

[26]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[27]  Agbessi Amouzou,et al.  Monitoring Change in Child Mortality through Household Surveys , 2015, PloS one.

[28]  S. MacFeely Measuring the Sustainable Development Goal Indicators: An Unprecedented Statistical Challenge , 2020, Journal of Official Statistics.

[29]  D. Binder On the variances of asymptotically normal estimators from complex surveys , 1983 .

[30]  Jon Wakefield,et al.  Small Area Estimation of Child Mortality in the Absence of Vital Registration , 2014 .

[31]  Leonhard Held,et al.  Gaussian Markov Random Fields: Theory and Applications , 2005 .