A Bayesian latent process spatiotemporal regression model for areal count data

Leveraging a national biorepository in Zambia to assess measles and rubella immunity gaps across age and space

High-quality, representative serological surveys allow direct estimates of immunity profiles to inform vaccination strategies but can be costly and logistically challenging. Leveraging residual serum samples is one way to increase their feasibility. We subsampled 9854 residual sera from a 2016 national HIV survey in Zambia and tested these specimens for anti-measles and anti-rubella virus IgG antibodies using indirect enzyme immunoassays. We demonstrate innovative methods for sampling residual sera and analyzing seroprevalence data, as well as the value of seroprevalence estimates to understand and control measles and rubella. National measles and rubella seroprevalence for individuals younger than 50 years was 82.8% (95% CI 81.6, 83.9%) and 74.9% (95% CI 73.7, 76.0%), respectively. Despite a successful childhood vaccination program, measles immunity gaps persisted across age groups and districts, indicating the need for additional activities to complement routine immunization. Prior to vaccine introduction, we estimated a rubella burden of 96 congenital rubella syndrome cases per 100,000 live births. Residual samples from large-scale surveys can reduce the cost and challenges of conducting serosurveys, and multiple pathogens can be tested. Procedures to access quality specimens, ensure ethical approvals, and link sociodemographic data can improve the timeliness and value of results.

Practical geospatial and sociodemographic predictors of human mobility

Understanding seasonal human mobility at subnational scales has important implications across sciences, from urban planning efforts to disease modelling and control. Assessing how, when, and where populations move over the course of the year, however, requires spatially and temporally resolved datasets spanning large periods of time, which can be rare, contain sensitive information, or may be proprietary. Here, we aim to explore how a set of broadly available covariates can describe typical seasonal subnational mobility in Kenya pre-COVID-19, therefore enabling better modelling of seasonal mobility across low- and middle-income country (LMIC) settings in non-pandemic settings. To do this, we used the Google Aggregated Mobility Research Dataset, containing anonymized mobility flows aggregated over users who have turned on the Location History setting, which is off by default. We combined this with socioeconomic and geospatial covariates from 2018 to 2019 to quantify seasonal changes in domestic and international mobility patterns across years. We undertook a spatiotemporal analysis within a Bayesian framework to identify relevant geospatial and socioeconomic covariates explaining human movement patterns, while accounting for spatial and temporal autocorrelations. Typical pre-pandemic mobility patterns in Kenya mostly consisted of shorter, within-county trips, followed by longer domestic travel between counties and international travel, which is important in establishing how mobility patterns changed post-pandemic. Mobility peaked in August and December, closely corresponding to school holiday seasons, which was found to be an important predictor in our model. We further found that socioeconomic variables including urbanicity, poverty, and female education strongly explained mobility patterns, in addition to geospatial covariates such as accessibility to major population centres and temperature. These findings derived from novel data sources elucidate broad spatiotemporal patterns of how populations move within and beyond Kenya, and can be easily generalized to other LMIC settings before the COVID-19 pandemic. Understanding such pre-pandemic mobility patterns provides a crucial baseline to interpret both how these patterns have changed as a result of the pandemic, as well as whether human mobility patterns have been permanently altered once the pandemic subsides. Our findings outline key correlates of mobility using broadly available covariates, alleviating the data bottlenecks of highly sensitive and proprietary mobile phone datasets, which many researchers do not have access to. These results further provide novel insight on monitoring mobility proxies in the context of disease surveillance and control efforts through LMIC settings.

Analysing Normative Influences on the Prevalence of Female Genital Mutilation/Cutting among 0-14 Years Old Girls in Senegal: A Spatial Bayesian Hierarchical Regression Approach

BACKGROUND

Female genital mutilation/cutting (FGM/C) is a harmful traditional practice affecting the health and rights of women and girls. This has raised global attention on the implementation of strategies to eliminate the practice in conformity with the Sustainable Development Goals (SDGs). A recent study on the trends of FGM/C among Senegalese women (aged 15-49) which examined how individual- and community-level factors affected the practice, found significant regional variations in the practice. However, the dynamics of the practice among girls (0-14 years old) is not fully understood. This paper attempts to fill this knowledge gap by investigating normative influences in the persistence of the practice among Senegalese girls, identify and map 'hotspots'.

METHODS

We do so by using a class of Bayesian hierarchical geospatial modelling approach implemented in R statistical software (R Foundation for Statistical Computing, Vienna, Austria) using R2BayesX package. We employed Markov Chain Monte Carlo (MCMC) techniques for full Bayesian inference, while model fit and complexity assessment utilised deviance information criterion (DIC).

RESULTS

We found that a girl's probability of cutting was higher if her mother was cut, supported FGM/C continuation or believed that the practice was a religious obligation. In addition, living in rural areas and being born to a mother from Diola, Mandingue, Soninke or Poular ethnic group increased a girl's likelihood of being cut. The hotspots identified included Matam, Tambacounda and Kolda regions.

CONCLUSIONS

Our findings offer a clearer picture of the dynamics of FGM/C practice among Senegalese girls and prove useful in informing evidence-based intervention policies designed to achieve the abandonment of the practice in Senegal.

Evaluating changes in the prevalence of female genital mutilation/cutting among 0-14 years old girls in Nigeria using data from multiple surveys: A novel Bayesian hierarchical spatio-temporal model

Female genital mutilation/cutting (FGM/C) is considered a public health and human rights concern, mainly concentrated in Africa, and has been targeted for elimination under the sustainable development goals. Interventions aimed at ending the practice often rely on data from household surveys which employ complex designs leading to outcomes that are not totally independent, thus requiring advanced statistical techniques. Combining data from multiple surveys within robust statistical framework holds promise to provide more precise estimates due to increased sample size, and accurately identify ‘hotspots’ and allow for assessment of changes over time. In this study, rich datasets from six (6) successive waves of the Nigeria Demographic and Health Surveys and Multiple Indicator Cluster Surveys undertaken between 2003 and 2016/17, were combined and analyzed in order to better assess changes in the likelihood and prevalence of FGM/C among 0-14-year old girls in Nigeria. We used Bayesian hierarchical regression models which explicitly accounted for the inherent spatial and temporal autocorrelations within the data while simultaneously adjusting for variations due to different survey methods and the effects of linear and non-linear covariates. Parameters were estimated using Markov chain Mote Carlo techniques and model fit assessments were based on Deviance Information Criterion. Results show that prevalence of FGM/C among 0–14 years old girls in Nigeria varied over time and across geographical locations and peaked in 2008 with a shift from South to North. A girl was more likely to be cut if her mother was cut, supported FGM/C continuation, or had no higher education. The effects of mother’s age, wealth and type of residence (urban-rural) were no longer significant in 2016. These results reflect the gains of interventions over the years, but also echo the belief that FGM/C is a social norm thus requiring tailored all-inclusive interventions for the total abandonment of FGM/C in Nigeria.

A systematic review of Bayesian spatial-temporal models on cancer incidence and mortality

OBJECTIVES

This study aimed to review the types and applications of fully Bayesian (FB) spatial-temporal models and covariates used to study cancer incidence and mortality.

METHODS

This systematic review searched articles published within Medline, Embase, Web-of-Science and Google Scholar between 2014 and 2018.

RESULTS

A total of 38 studies were included in our study. All studies applied Bayesian spatial-temporal models to explore spatial patterns over time, and over half assessed the association with risk factors. Studies used different modelling approaches and prior distributions for spatial, temporal and spatial-temporal interaction effects depending on the nature of data, outcomes and applications. The most common Bayesian spatial-temporal model was a generalized linear mixed model. These models adjusted for covariates at the patient, area or temporal level, and through standardization.

CONCLUSIONS

Few studies (4) modelled patient-level clinical characteristics (11%), and the applications of an FB approach in the forecasting of spatial-temporally aligned cancer data were limited. This review highlighted the need for Bayesian spatial-temporal models to incorporate patient-level prognostic characteristics through the multi-level framework and forecast future cancer incidence and outcomes for cancer prevention and control strategies.

A Spatial Analysis of the Prevalence of Female Genital Mutilation/Cutting among 0-14-Year-Old Girls in Kenya

Female genital mutilation/cutting (FGM/C), also known as female circumcision, is a global public health and human rights problem affecting women and girls. Several concerted efforts to eliminate the practice are underway in several sub-Saharan African countries where the practice is most prevalent. Studies have reported variations in the practice with some countries experiencing relatively slow decline in prevalence. This study investigates the roles of normative influences and related risk factors (e.g., geographic location) on the persistence of FGM/C among 0–14 years old girls in Kenya. The key objective is to identify and map hotspots (high risk regions). We fitted spatial and spatio-temporal models in a Bayesian hierarchical regression framework on two datasets extracted from successive Kenya Demographic and Health Surveys (KDHS) from 1998 to 2014. The models were implemented in R statistical software using Markov Chain Monte Carlo (MCMC) techniques for parameters estimation, while model fit and assessment employed deviance information criterion (DIC) and effective sample size (ESS). Results showed that daughters of cut women were highly likely to be cut. Also, the likelihood of a girl being cut increased with the proportion of women in the community (1) who were cut (2) who supported FGM/C continuation, and (3) who believed FGM/C was a religious obligation. Other key risk factors included living in the northeastern region; belonging to the Kisii or Somali ethnic groups and being of Muslim background. These findings offered a clearer picture of the dynamics of FGM/C in Kenya and will aid targeted interventions through bespoke policymaking and implementations.