The spread of COVID-19 makes it essential to investigate its prevalence. In such investigation research, as far as we know, the widely-used sampling methods didn't use the information sufficiently about the numbers of the previously diagnosed cases, which provides a priori information about the true numbers of infections. This motivates us to develop a new, two-stage sampling method in this paper, which utilises the information about the distributions of both population and diagnosed cases, to investigate the prevalence more efficiently. The global likelihood sampling, a robust and efficient sampler to draw samples from any probability density function, is used in our sampling strategy, and thus, our new method can automatically adapt to the complicated distributions of population and cases. Moreover, the corresponding estimating method is simple, which facilitates the practical implementation. Some recommendations for practical implementation are given. Finally, several simulations and a practical example verified its efficiency.
Background: Guidelines and recommendations from public health authorities related to face masks have been essential in containing the COVID-19 pandemic. We assessed the prevalence and correlates of mask usage during the pandemic. Methods: We examined a total of 13,723,810 responses to a daily cross-sectional representative online survey in 38 countries who completed from April 23, 2020 to October 31, 2020 and reported having been in public at least once during the last seven days. The outcome was individual face mask usage in public settings, and the predictors were country fixed effects, coun…
We present an extension of the Li and Lee model to quantify mortality in five European countries during the COVID-19 pandemic. The first two factors are used to model the pre-COVID mortality, with the first layer modelling the common trend and the second layer the country-specific deviation from the common trend. We add a third layer to capture the country-specific impact of COVID-19 in 2020 and 2021 in excess of the pre-COVID trend. We use weekly mortality data from the Short Term Mortality Fluctuations Database to calibrate this third factor, and we use a more granular dataset for deaths in …
Ending the HIV/AIDS pandemic is among the Sustainable Development Goals for the next decade. In order to overcome the gap between the need for care and the available resources, better understanding of HIV epidemics is needed to guide policy decisions, especially for key populations that are at higher risk for HIV infection. Accurate HIV epidemic estimates for key populations have been difficult to obtain because their HIV surveillance data is very limited. In this paper, we propose a so-called joint spatial conditional auto-regressive model for estimating HIV prevalence rates among key populat…
COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends, temperature, and spatio-temporal patterns. In addition to this, high geographical resolution is required to examine within country trends and the effectiveness of the different public health policies. In this tutorial, we propose a framework using R …
In wake of the Covid-19 pandemic, 2019-2020 soccer seasons across the world were postponed and eventually made up during the summer months of 2020. Researchers from a variety of disciplines jumped at the opportunity to compare the rescheduled games, played in front of empty stadia, to previous games, played in front of fans. To date, most of this post-Covid soccer research has used linear regression models, or versions thereof, to estimate potential changes to the home advantage. But because soccer outcomes are non-linear, we argue that leveraging the Poisson distribution would be more appropr…
To make informative public policy decisions in battling the ongoing COVID-19 pandemic, it is important to know the disease prevalence in a population. There are two intertwined difficulties in estimating this prevalence based on testing results from a group of subjects. First, the test is prone to measurement error with unknown sensitivity and specificity. Second, the prevalence tends to be low at the initial stage of the pandemic and we may not be able to determine if a positive test result is a false positive due to the imperfect specificity of the test. The statistical inference based on la…
A Bayesian Multiscale Integrated Abundance Model for Estimating Latent Opioid Misuse Prevalence from Spatially Misaligned Data
Wake Forest University（维克森林大学）；Wake Forest University School of Medicine（维克森林大学医学院）；Yale School of Public Health（耶鲁公共卫生学院）；Gillings School of Public Health, University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校吉林斯公共卫生学院）；Rollins School of Public Health, Emory University（埃默里大学罗林斯公共卫生学院）
A Counterfactual Framework for Estimating Infectious Disease Prevalence under Repeated Testing with Symptomatic and Contact-Tracing Components
Division of Biostatistics, College of Public Health, The Ohio State University（俄亥俄州立大学公共卫生学院生物统计系）；Department of Medical Epidemiology and Biostatistics, Karolinska Institutet（卡罗林斯卡医学院医学流行病学与生物统计系）
The effective reproduction number is a key figure to monitor the course of the COVID-19 pandemic. In this study we consider a retrospective modelling approach for estimating the effective reproduction number based on death counts during the first year of the pandemic in Germany. The proposed Bayesian hierarchical model incorporates splines to estimate reproduction numbers flexibly over time while adjusting for varying effective infection fatality rates. The approach also provides estimates of dark figures regarding undetected infections over time. Results for Germany illustrate that estimated …
The present paper introduces a new model used to study and analyse the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) epidemic-reported-data from Spain. This is a Hidden Markov Model whose hidden layer is a regeneration process with Poisson immigration, Po-INAR(1), together with a mechanism that allows the estimation of the under-reporting in non-stationary count time series. A novelty of the model is that the expectation of the innovations in the unobserved process is a time-dependent function defined in such a way that information about the spread of an epidemic, as modelled thr…
The infection fatality rate (IFR) of the Coronavirus Disease 2019 (COVID-19) is one of the most discussed figures in the context of this pandemic. Using German COVID-19 surveillance data and age-group specific IFR estimates from multiple international studies, this work investigates time-dependent variations in effective IFR over the course of the pandemic. Three different methods for estimating (effective) IFRs are presented: (a) population-averaged IFRs based on the assumption that the infection risk is independent of age and time, (b) effective IFRs based on the assumption that the age dist…
Large-scale testing is considered key to assess the state of the current COVID-19 pandemic. Yet, the link between the reported case numbers and the true state of the pandemic remains elusive. We develop mathematical models based on competing hypotheses regarding this link, thereby providing different prevalence estimates based on case numbers, and validate them by predicting SARS-CoV-2-attributed death rate trajectories. Assuming that individuals were tested based solely on a predefined risk of being infectious implies the absolute case numbers reflect the prevalence, but turned out to be a po…
The COVID-19 pandemic has led to a vast amount of growth for statistical models and methods which characterize features of disease outbreaks. One class of models that came to light in this regard has been the use of self-exciting point processes, wherein infections occur both "at random" and also more systematically from person-to-person transmission. Beyond the modeling of the overall COVID-19 outbreak, the pandemic has also motivated research assessing various policy decisions and event outcomes. One such area of study, addressed here, relates to the formulation of methods which measure the …
The current outbreak of COVID-19 has called renewed attention to the need for sound statistical analysis for monitoring mortality patterns and trends over time. Excess mortality has been suggested as the most appropriate indicator to measure the overall burden of the pandemic on mortality. As such, excess mortality has received considerable interest during the first months of the COVID-19 pandemic. Previous approaches to estimate excess mortality are somewhat limited, as they do not include sufficiently long-term trends, correlations among different demographic and geographic groups, and the a…
There are many sources of data giving information about the number of SARS-CoV-2 infections in the population, but all have major drawbacks, including biases and delayed reporting. For example, the number of confirmed cases largely underestimates the number of infections, deaths lag infections substantially, while test positivity rates tend to greatly overestimate prevalence. Representative random prevalence surveys, the only putatively unbiased source, are sparse in time and space, and the results come with a big delay. Reliable estimates of population prevalence are necessary for understandi…
This paper introduces an alternative procedure for estimating the prevalence of international migration at the municipal level in Colombia. The new methodology uses the empirical best linear unbiased predictor based on a Fay-Herriot model with target and auxiliary variables available from census studies and from the Demographic and Health Survey. The proposed alternative produces prevalence estimates which are consistent with sample sizes and demographic dynamics in Colombia. Additionally, the estimated coefficients of variation are lower than 20% for municipalities and large demographically-r…
Intuitively, sampling is likely to be more efficient for prevalence estimation, if the cases (or positives) have a relatively higher representation in the sample than in the population. In case the virus is transmitted via personal contacts, contact tracing of the observed cases (but not noncases), to be referred to as \emph{adaptive network tracing}, can generate a higher yield of cases than random sampling from the population. The efficacy of relevant designs for cross-sectional and change estimation is investigated. The availability of these designs allows one unite tracing for combating th…
Estimating the true mortality burden of COVID-19 for every country in the world is a difficult, but crucial, public health endeavor. Attributing deaths, direct or indirect, to COVID-19 is problematic. A more attainable target is the "excess deaths", the number of deaths in a particular period, relative to that expected during "normal times", and we estimate this for all countries on a monthly time scale for 2020 and 2021. The excess mortality requires two numbers, the total deaths and the expected deaths, but the former is unavailable for many countries, and so modeling is required for these c…
We consider the problem of estimating the reproduction number $R_t$ of an epidemic for populations where the probability of detection of cases depends on a known covariate. We argue that in such cases the normal empirical estimator can fail when the prevalence of cases among groups changes with time. We propose a Bayesian strategy to resolve the problem, as well as a simple solution in the case of large number of cases. We illustrate the issue and its solution on a simple yet realistic simulation study, and discuss the general relevance of the issue to the current covid19 pandemic.
Serology testing can identify past infection by quantifying the immune response of an infected individual providing important public health guidance. Individual immune responses are time-dependent, which is reflected in antibody measurements. Moreover, the probability of obtaining a particular measurement changes due to prevalence as the disease progresses. Taking into account these personal and population-level effects, we develop a mathematical model that suggests a natural adaptive scheme for estimating prevalence as a function of time. We then combine the estimated prevalence with optimal …
Bayesian adaptive designs have gained popularity in all phases of clinical trials with numerous new developments in the past few decades. During the COVID-19 pandemic, the need to establish evidence for the effectiveness of vaccines, therapeutic treatments and policies that could resolve or control the crisis emphasized the advantages offered by efficient and flexible clinical trial designs. In many COVID-19 clinical trials, due to the high level of uncertainty, Bayesian adaptive designs were considered advantageous. Designing Bayesian adaptive trials, however, requires extensive simulation st…
As the global HIV pandemic enters its fourth decade, increasing numbers of surveillance sites have been established which allows countries to look into the epidemics at a finer scale, e.g. at sub-national levels. Currently, the epidemic models have been applied independently to the sub-national areas within countries. However, the availability and quality of the data vary widely, which leads to biased and unreliable estimates for areas with very few data. We propose to overcome this issue by introducing the dependence of the parameters across areas in a mixture model. The joint distribution of…
We investigate the problem of estimating the distribution of the individual reproduction number governing the COVID-19 pandemic. Under the assumption that this random variable follows a Negative Binomial distribution, we focus on constructing estimators of the parameters of this distribution using reported infection data and taking into account issues like under-reporting or the time behavior of the infection and of the reporting processes. To this end, we extract information from regionally dissaggregated data reported by German health authorities, in order to estimate not only the mean but a…
We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdict…
In August 2020, as Texas was coming down from a large summer COVID-19 surge, forecasts suggested that Hurricane Laura was tracking towards 6M residents along the East Texas coastline, threatening to spread COVID-19 across the state and cause pandemic resurgences. To assist local authorities facing the dual-threat, we integrated survey expectations of coastal residents and observed hurricane evacuation rates in a statistical framework that combined with local pandemic conditions predicts how COVID-19 would spread in response to a hurricane. For Hurricane Laura, we estimate that 499,500 [90% Cre…
University of Ibadan（伊巴丹大学）；University College Hospital, Ibadan（伊巴丹大学学院医院）；University College London（伦敦大学学院）
Plasmodium falciparum malaria still poses one of the greatest threats to human life with over 200 million cases globally leading to half-million deaths annually. Of these, 90% of cases and of the mortality occurs in sub-Saharan Africa, mostly among children. Although malaria prediction systems are central to the 2016-2030 malaria Global Technical Strategy, currently these are inadequate at capturing and estimating the burden of disease in highly endemic countries. We developed and validated a computational system that exploits the predictive power of current Machine Learning approaches on 22-y…
Respondent-Driven Sampling (RDS) is an approach to sampling design and inference in hard-to-reach human populations. Typically, a sampling frame is not available, and population members are difficult to identify or recruit from broader sampling frames. Common examples include injecting drug users, men who have sex with men, and female sex workers. Most analysis of RDS data has focused on estimating aggregate characteristics, such as disease prevalence. However, RDS is often conducted in settings where the population size is unknown and of great independent interest. This paper presents an appr…
