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  1. Article ; Online: Spatio-Temporal Bayesian Models for Malaria Risk Using Survey and Health Facility Routine Data in Rwanda.

    Semakula, Muhammed / Niragire, François / Faes, Christel

    International journal of environmental research and public health

    2023  Volume 20, Issue 5

    Abstract: Introduction: Malaria is a life-threatening disease ocuring mainly in developing countries. Almost half of the world's population was at risk of malaria in 2020. Children under five years age are among the population groups at considerably higher risk ... ...

    Abstract Introduction: Malaria is a life-threatening disease ocuring mainly in developing countries. Almost half of the world's population was at risk of malaria in 2020. Children under five years age are among the population groups at considerably higher risk of contracting malaria and developing severe disease. Most countries use Demographic and Health Survey (DHS) data for health programs and evaluation. However, malaria elimination strategies require a real-time, locally-tailored response based on malaria risk estimates at the lowest administrative levels. In this paper, we propose a two-step modeling framework using survey and routine data to improve estimates of malaria risk incidence in small areas and enable quantifying malaria trends.
    Methods: To improve estimates, we suggest an alternative approach to modeling malaria relative risk by combining information from survey and routine data through Bayesian spatio-temporal models. We model malaria risk using two steps: (1) fitting a binomial model to the survey data, and (2) extracting fitted values and using them in the Poison model as nonlinear effects in the routine data. We modeled malaria relative risk among under-five-year old children in Rwanda.
    Results: The estimation of malaria prevalence among children who are under five years old using Rwanda demographic and health survey data for the years 2019-2020 alone showed a higher prevalence in the southwest, central, and northeast of Rwanda than the rest of the country. Combining with routine health facility data, we detected clusters that were undetected based on the survey data alone. The proposed approach enabled spatial and temporal trend effect estimation of relative risk in local/small areas in Rwanda.
    Conclusions: The findings of this analysis suggest that using DHS combined with routine health services data for active malaria surveillance may provide provide more precise estimates of the malaria burden, which can be used toward malaria elimination targets. We compared findings from geostatistical modeling of malaria prevalence among under-five-year old children using DHS 2019-2020 and findings from malaria relative risk spatio-temporal modeling using both DHS survey 2019-2020 and health facility routine data. The strength of routinely collected data at small scales and high-quality data from the survey contributed to a better understanding of the malaria relative risk at the subnational level in Rwanda.
    MeSH term(s) Child ; Humans ; Child, Preschool ; Rwanda ; Bayes Theorem ; Malaria/epidemiology ; Probability ; Health Facilities ; Spatio-Temporal Analysis
    Language English
    Publishing date 2023-02-28
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2175195-X
    ISSN 1660-4601 ; 1661-7827
    ISSN (online) 1660-4601
    ISSN 1661-7827
    DOI 10.3390/ijerph20054283
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A practical illustration of spatial smoothing methods for disconnected regions with INLA: spatial survey on overweight and obesity in Malaysia.

    Mohamad, Maria Safura / Abdul Maulud, Khairul Nizam / Faes, Christel

    International journal of health geographics

    2023  Volume 22, Issue 1, Page(s) 14

    Abstract: Background: National prevalence could mask subnational heterogeneity in disease occurrence, and disease mapping is an important tool to illustrate the spatial pattern of disease. However, there is limited information on techniques for the specification ... ...

    Abstract Background: National prevalence could mask subnational heterogeneity in disease occurrence, and disease mapping is an important tool to illustrate the spatial pattern of disease. However, there is limited information on techniques for the specification of conditional autoregressive models in disease mapping involving disconnected regions. This study explores available techniques for producing district-level prevalence estimates for disconnected regions, using as an example childhood overweight in Malaysia, which consists of the Peninsular and Borneo regions separated by the South China Sea. We used data from Malaysia National Health and Morbidity Survey conducted in 2015. We adopted Bayesian hierarchical modelling using the integrated nested Laplace approximation (INLA) program in R-software to model the spatial distribution of overweight among 6301 children aged 5-17 years across 144 districts located in two disconnected regions. We illustrate different types of spatial models for prevalence mapping across disconnected regions, taking into account the survey design and adjusting for district-level demographic and socioeconomic covariates.
    Results: The spatial model with split random effects and a common intercept has the lowest Deviance and Watanabe Information Criteria. There was evidence of a spatial pattern in the prevalence of childhood overweight across districts. An increasing trend in smoothed prevalence of overweight was observed when moving from the east to the west of the Peninsular and Borneo regions. The proportion of Bumiputera ethnicity in the district had a significant negative association with childhood overweight: the higher the proportion of Bumiputera ethnicity in the district, the lower the prevalence of childhood overweight.
    Conclusion: This study illustrates different available techniques for mapping prevalence across districts in disconnected regions using survey data. These techniques can be utilized to produce reliable subnational estimates for any areas that comprise of disconnected regions. Through the example, we learned that the best-fit model was the one that considered the separate variations of the individual regions. We discovered that the occurrence of childhood overweight in Malaysia followed a spatial pattern with an east-west gradient trend, and we identified districts with high prevalence of overweight. This information could help policy makers in making informed decisions for targeted public health interventions in high-risk areas.
    MeSH term(s) Child ; Humans ; Bayes Theorem ; Malaysia/epidemiology ; Pediatric Obesity/epidemiology ; Prevalence ; Child, Preschool ; Adolescent ; Health Surveys ; Spatial Analysis ; Male ; Female
    Language English
    Publishing date 2023-06-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2091613-9
    ISSN 1476-072X ; 1476-072X
    ISSN (online) 1476-072X
    ISSN 1476-072X
    DOI 10.1186/s12942-023-00336-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An approximate Bayesian approach for estimation of the instantaneous reproduction number under misreported epidemic data.

    Gressani, Oswaldo / Faes, Christel / Hens, Niel

    Biometrical journal. Biometrische Zeitschrift

    2023  Volume 65, Issue 6, Page(s) e2200024

    Abstract: In epidemic models, the effective reproduction number is of central importance to assess the transmission dynamics of an infectious disease and to orient health intervention strategies. Publicly shared data during an outbreak often suffers from two ... ...

    Abstract In epidemic models, the effective reproduction number is of central importance to assess the transmission dynamics of an infectious disease and to orient health intervention strategies. Publicly shared data during an outbreak often suffers from two sources of misreporting (underreporting and delay in reporting) that should not be overlooked when estimating epidemiological parameters. The main statistical challenge in models that intrinsically account for a misreporting process lies in the joint estimation of the time-varying reproduction number and the delay/underreporting parameters. Existing Bayesian approaches typically rely on Markov chain Monte Carlo algorithms that are extremely costly from a computational perspective. We propose a much faster alternative based on Laplacian-P-splines (LPS) that combines Bayesian penalized B-splines for flexible and smooth estimation of the instantaneous reproduction number and Laplace approximations to selected posterior distributions for fast computation. Assuming a known generation interval distribution, the incidence at a given calendar time is governed by the epidemic renewal equation and the delay structure is specified through a composite link framework. Laplace approximations to the conditional posterior of the spline vector are obtained from analytical versions of the gradient and Hessian of the log-likelihood, implying a drastic speed-up in the computation of posterior estimates. Furthermore, the proposed LPS approach can be used to obtain point estimates and approximate credible intervals for the delay and reporting probabilities. Simulation of epidemics with different combinations for the underreporting rate and delay structure (one-day, two-day, and weekend delays) show that the proposed LPS methodology delivers fast and accurate estimates outperforming existing methods that do not take into account underreporting and delay patterns. Finally, LPS is illustrated in two real case studies of epidemic outbreaks.
    MeSH term(s) Humans ; Bayes Theorem ; Lipopolysaccharides ; Computer Simulation ; Communicable Diseases/epidemiology ; Epidemics ; Monte Carlo Method
    Chemical Substances Lipopolysaccharides
    Language English
    Publishing date 2023-01-13
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 131640-0
    ISSN 1521-4036 ; 0323-3847 ; 0006-3452
    ISSN (online) 1521-4036
    ISSN 0323-3847 ; 0006-3452
    DOI 10.1002/bimj.202200024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Cluster pattern analysis of environmental stressors and quantifying their impact on all-cause mortality in Belgium.

    Vandeninden, Bram / De Clercq, Eva M / Devleesschauwer, Brecht / Otavova, Martina / Bouland, Catherine / Faes, Christel

    BMC public health

    2024  Volume 24, Issue 1, Page(s) 536

    Abstract: Environmental stress represents an important burden on health and leads to a considerable number of diseases, hospitalisations, and excess mortality. Our study encompasses a representative sample size drawn from the Belgian population in 2016 (n = 11.26 ... ...

    Abstract Environmental stress represents an important burden on health and leads to a considerable number of diseases, hospitalisations, and excess mortality. Our study encompasses a representative sample size drawn from the Belgian population in 2016 (n = 11.26 million, with a focus on n = 11.15 million individuals). The analysis is conducted at the geographical level of statistical sectors, comprising a total of n = 19,794 sectors, with a subset of n = 18,681 sectors considered in the investigation. We integrated multiple parameters at the finest spatial level and constructed three categories of environmental stress through clustering: air pollution, noise stress and stress related to specific land-use types. We observed identifiable patterns in the spatial distribution of stressors within each cluster category. We assessed the relationship between age-standardized all-cause mortality rates (ASMR) and environmental stressors. Our research found that especially very high air pollution values in areas where traffic is the dominant local component of air pollution (ASMR + 14,8%, 95% CI: 10,4 - 19,4%) and presence of industrial land (ASMR + 14,7%, 95% CI: 9,4 - 20,2%) in the neighbourhood are associated with an increased ASMR. Cumulative exposure to multiple sources of unfavourable environmental stress (simultaneously high air pollution, high noise, presence of industrial land or proximity of primary/secondary roads and lack of green space) is associated with an increase in ASMR (ASMR + 26,9%, 95% CI: 17,1 - 36,5%).
    MeSH term(s) Humans ; Air Pollutants/analysis ; Belgium/epidemiology ; Air Pollution/adverse effects ; Air Pollution/analysis ; Noise/adverse effects ; Cluster Analysis ; Environmental Exposure/adverse effects ; Environmental Exposure/analysis ; Particulate Matter/analysis
    Chemical Substances Air Pollutants ; Particulate Matter
    Language English
    Publishing date 2024-02-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-024-18011-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Spatio-temporal dynamic of the COVID-19 epidemic and the impact of imported cases in Rwanda.

    Semakula, Muhammed / Niragire, François / Nsanzimana, Sabin / Remera, Eric / Faes, Christel

    BMC public health

    2023  Volume 23, Issue 1, Page(s) 930

    Abstract: Introduction: Africa was threatened by the coronavirus disease 2019 (COVID-19) due to the limited health care infrastructure. Rwanda has consistently used non-pharmaceutical strategies, such as lockdown, curfew, and enforcement of prevention measures to ...

    Abstract Introduction: Africa was threatened by the coronavirus disease 2019 (COVID-19) due to the limited health care infrastructure. Rwanda has consistently used non-pharmaceutical strategies, such as lockdown, curfew, and enforcement of prevention measures to control the spread of COVID-19. Despite the mitigation measures taken, the country has faced a series of outbreaks in 2020 and 2021. In this paper, we investigate the nature of epidemic phenomena in Rwanda and the impact of imported cases on the spread of COVID-19 using endemic-epidemic spatio-temporal models. Our study provides a framework for understanding the dynamics of the epidemic in Rwanda and monitoring its phenomena to inform public health decision-makers for timely and targeted interventions.
    Results: The findings provide insights into the effects of lockdown and imported infections in Rwanda's COVID-19 outbreaks. The findings showed that imported infections are dominated by locally transmitted cases. The high incidence was predominant in urban areas and at the borders of Rwanda with its neighboring countries. The inter-district spread of COVID-19 was very limited due to mitigation measures taken in Rwanda.
    Conclusion: The study recommends using evidence-based decisions in the management of epidemics and integrating statistical models in the analytics component of the health information system.
    MeSH term(s) Humans ; Rwanda ; Communicable Diseases, Imported ; COVID-19 ; Communicable Disease Control ; Epidemics
    Language English
    Publishing date 2023-05-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-15888-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Variation in smoking attributable all-cause mortality across municipalities in Belgium, 2018: application of a Bayesian approach for small area estimations.

    Putrik, Polina / Otavova, Martina / Faes, Christel / Devleesschauwer, Brecht

    BMC public health

    2022  Volume 22, Issue 1, Page(s) 1699

    Abstract: Background: Smoking is one of the leading causes of preventable mortality and morbidity worldwide, with the European Region having the highest prevalence of tobacco smoking among adults compared to other WHO regions. The Belgian Health Interview Survey ( ...

    Abstract Background: Smoking is one of the leading causes of preventable mortality and morbidity worldwide, with the European Region having the highest prevalence of tobacco smoking among adults compared to other WHO regions. The Belgian Health Interview Survey (BHIS) provides a reliable source of national and regional estimates of smoking prevalence; however, currently there are no estimates at a smaller geographical resolution such as the municipality scale in Belgium. This hinders the estimation of the spatial distribution of smoking attributable mortality at small geographical scale (i.e., number of deaths that can be attributed to tobacco). The objective of this study was to obtain estimates of smoking prevalence in each Belgian municipality using BHIS and calculate smoking attributable mortality at municipality level.
    Methods: Data of participants aged 15 + on smoking behavior, age, gender, educational level and municipality of residence were obtained from the BHIS 2018. A Bayesian hierarchical Besag-York-Mollie (BYM) model was used to model the logit transformation of the design-based Horvitz-Thompson direct prevalence estimates. Municipality-level variables obtained from Statbel, the Belgian statistical office, were used as auxiliary variables in the model. Model parameters were estimated using Integrated Nested Laplace Approximation (INLA). Deviance Information Criterion (DIC) and Conditional Predictive Ordinate (CPO) were computed to assess model fit. Population attributable fractions (PAF) were computed using the estimated prevalence of smoking in each of the 589 Belgian municipalities and relative risks obtained from published meta-analyses. Smoking attributable mortality was calculated by multiplying PAF with age-gender standardized and stratified number of deaths in each municipality.
    Results: BHIS 2018 data included 7,829 respondents from 154 municipalities. Smoothed estimates for current smoking ranged between 11% [Credible Interval 3;23] and 27% [21;34] per municipality, and for former smoking between 4% [0;14] and 34% [21;47]. Estimates of smoking attributable mortality constituted between 10% [7;15] and 47% [34;59] of total number of deaths per municipality.
    Conclusions: Within-country variation in smoking and smoking attributable mortality was observed. Computed estimates should inform local public health prevention campaigns as well as contribute to explaining the regional differences in mortality.
    MeSH term(s) Adult ; Bayes Theorem ; Belgium/epidemiology ; Cities ; Humans ; Smoking/epidemiology ; Tobacco Smoking
    Language English
    Publishing date 2022-09-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-022-14067-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: HIV risk factors among adolescent and young adults: A geospatial-temporal analysis of Mozambique AIDS indicator survey data.

    Muleia, Rachid / Aerts, Marc / Loquiha, Osvaldo / Faes, Christel

    Spatial and spatio-temporal epidemiology

    2022  Volume 41, Page(s) 100499

    Abstract: In a developing country, it is very crucial to know where the HIV/AIDS epidemic is much more prevalent and where direct interventions are needed, especially when managing limited and scarce resources. We therefore examine the spatial distribution of HIV ... ...

    Abstract In a developing country, it is very crucial to know where the HIV/AIDS epidemic is much more prevalent and where direct interventions are needed, especially when managing limited and scarce resources. We therefore examine the spatial distribution of HIV in Mozambique, and also assess how the epidemic evolved over a six-year period (2009-2015), with respect to potential risk factors among adolescents and young adults. We used data from the 2009 and 2015 Mozambique AIDS indicator surveys. The data were analysed jointly, by extending the work of Muleia et al. (2020) to allow for different bivariate spatial smoothing functions for both surveys. The results showed considerable spatial variation. From 2009 to 2015, the probability to be HIV positive reduced by 43.6% for young women. The results also showed dependence of the probability for HIV infection on sociodemographic factors. The findings herein will help health officials design efficient target interventions.
    MeSH term(s) Acquired Immunodeficiency Syndrome/epidemiology ; Adolescent ; Epidemics ; Female ; HIV Infections/epidemiology ; Humans ; Mozambique/epidemiology ; Risk Factors ; Young Adult
    Language English
    Publishing date 2022-03-19
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2515896-X
    ISSN 1877-5853 ; 1877-5845
    ISSN (online) 1877-5853
    ISSN 1877-5845
    DOI 10.1016/j.sste.2022.100499
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Laplacian-P-splines for Bayesian inference in the mixture cure model.

    Gressani, Oswaldo / Faes, Christel / Hens, Niel

    Statistics in medicine

    2022  Volume 41, Issue 14, Page(s) 2602–2626

    Abstract: The mixture cure model for analyzing survival data is characterized by the assumption that the population under study is divided into a group of subjects who will experience the event of interest over some finite time horizon and another group of cured ... ...

    Abstract The mixture cure model for analyzing survival data is characterized by the assumption that the population under study is divided into a group of subjects who will experience the event of interest over some finite time horizon and another group of cured subjects who will never experience the event irrespective of the duration of follow-up. When using the Bayesian paradigm for inference in survival models with a cure fraction, it is common practice to rely on Markov chain Monte Carlo (MCMC) methods to sample from posterior distributions. Although computationally feasible, the iterative nature of MCMC often implies long sampling times to explore the target space with chains that may suffer from slow convergence and poor mixing. Furthermore, extra efforts have to be invested in diagnostic checks to monitor the reliability of the generated posterior samples. A sampling-free strategy for fast and flexible Bayesian inference in the mixture cure model is suggested in this article by combining Laplace approximations and penalized B-splines. A logistic regression model is assumed for the cure proportion and a Cox proportional hazards model with a P-spline approximated baseline hazard is used to specify the conditional survival function of susceptible subjects. Laplace approximations to the posterior conditional latent vector are based on analytical formulas for the gradient and Hessian of the log-likelihood, resulting in a substantial speed-up in approximating posterior distributions. The spline specification yields smooth estimates of survival curves and functions of latent variables together with their associated credible interval are estimated in seconds. A fully stochastic algorithm based on a Metropolis-Langevin-within-Gibbs sampler is also suggested as an alternative to the proposed Laplacian-P-splines mixture cure (LPSMC) methodology. The statistical performance and computational efficiency of LPSMC is assessed in a simulation study. Results show that LPSMC is an appealing alternative to MCMC for approximate Bayesian inference in standard mixture cure models. Finally, the novel LPSMC approach is illustrated on three applications involving real survival data.
    MeSH term(s) Algorithms ; Bayes Theorem ; Humans ; Markov Chains ; Monte Carlo Method ; Proportional Hazards Models ; Reproducibility of Results
    Language English
    Publishing date 2022-03-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 843037-8
    ISSN 1097-0258 ; 0277-6715
    ISSN (online) 1097-0258
    ISSN 0277-6715
    DOI 10.1002/sim.9373
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Measles epidemic in Southern Vietnam: an age-stratified spatio-temporal model for infectious disease counts.

    Nguyen, Thi Huyen Trang / Faes, Christel / Hens, Niel

    Epidemiology and infection

    2022  Volume 150, Page(s) e169

    Abstract: Measles resurged in Vietnam between 2018 and 2020, especially in the Southern region. The proportion of children with measles infection showed quite some variation at the provincial level. We applied a spatio-temporal endemic-epidemic modelling framework ...

    Abstract Measles resurged in Vietnam between 2018 and 2020, especially in the Southern region. The proportion of children with measles infection showed quite some variation at the provincial level. We applied a spatio-temporal endemic-epidemic modelling framework for age-stratified infectious disease counts using measles surveillance data collected in Southern Vietnam between 1 January 2018 and 30 June 2020. We found that disease transmission within age groups was greatest in young children aged 0-4 years whereas a relatively high between-group transmission was observed in older age groups (5-14 years, 15-24 years and 25+ years groups). At the provincial level, spatial transmission followed an age-dependent distance decay with measles spread mainly depending on local and neighbouring transmission. Our study helped to clarify the measles transmission dynamics in a more detailed fashion with respect to age strata, time and space. Findings from this study may help determine proper strategies in measles outbreak control including promotion of age-targeted intervention programmes in specific areas.
    MeSH term(s) Aged ; Child ; Child, Preschool ; Communicable Diseases/epidemiology ; Disease Outbreaks/prevention & control ; Epidemics ; Humans ; Measles/prevention & control ; Vietnam/epidemiology
    Language English
    Publishing date 2022-09-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 632982-2
    ISSN 1469-4409 ; 0950-2688
    ISSN (online) 1469-4409
    ISSN 0950-2688
    DOI 10.1017/S0950268822001431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A linear mixed model to estimate COVID‐19‐induced excess mortality

    Verbeeck, Johan / Faes, Christel / Neyens, Thomas / Hens, Niel / Verbeke, Geert / Deboosere, Patrick / Molenberghs, Geert

    Biometrics. 2023 Mar., v. 79, no. 1 p.417-425

    2023  

    Abstract: The Corona Virus Disease (COVID‐19) pandemic has increased mortality in countries worldwide. To evaluate the impact of the pandemic on mortality, the use of excess mortality rather than reported COVID‐19 deaths has been suggested. Excess mortality, ... ...

    Abstract The Corona Virus Disease (COVID‐19) pandemic has increased mortality in countries worldwide. To evaluate the impact of the pandemic on mortality, the use of excess mortality rather than reported COVID‐19 deaths has been suggested. Excess mortality, however, requires estimation of mortality under nonpandemic conditions. Although many methods exist to forecast mortality, they are either complex to apply, require many sources of information, ignore serial correlation, and/or are influenced by historical excess mortality. We propose a linear mixed model that is easy to apply, requires only historical mortality data, allows for serial correlation, and down‐weighs the influence of historical excess mortality. Appropriateness of the linear mixed model is evaluated with fit statistics and forecasting accuracy measures for Belgium and the Netherlands. Unlike the commonly used 5‐year weekly average, the linear mixed model is forecasting the year‐specific mortality, and as a result improves the estimation of excess mortality for Belgium and the Netherlands.
    Keywords COVID-19 infection ; autocorrelation ; mortality ; pandemic ; statistical models ; Belgium ; Netherlands
    Language English
    Dates of publication 2023-03
    Size p. 417-425.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 213543-7
    ISSN 0099-4987 ; 0006-341X
    ISSN 0099-4987 ; 0006-341X
    DOI 10.1111/biom.13578
    Database NAL-Catalogue (AGRICOLA)

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