Spatio-temporal models for count data are required in a wide range of scientific fields and they have become particularly crucial nowadays because of their ability to analyse COVID-19-related data. Models for count data are needed when the variable of interest take only non-negative integer values and these integers arise from counting occurrences. Several R-packages are currently available to deal with spatiotemporal areal count data. Each package focuses on different models and/or statistical methodologies. Unfortunately, the results generated by these models are rarely comparable due to differences in notation and methods. The main objective of this paper is to present a review describing the most important approaches that can be used to model and analyse count data when questions of scientific interest concern both their spatial and their temporal behaviour and we monitor their performance under the same data set.
For this review, we focus on the three R-packages that can be used for this purpose and the different models assessed are representative of the two most widespread methodologies used to analyse spatiotemporal count data: the classical approach (based on Penalised Likelihood or Estimating Equations) and the Bayesian point of view.
A case study is analysed as an illustration of these different methodologies. In this case study, these packages are used to model and predict daily hospitalisations from COVID-19 in 24 health regions within the Valencian Community (Spain), with data corresponding to the period from 28 June to 13 December 2020. Because of the current urgent need for monitoring and predicting data in the COVID-19 pandemic, this case study is, in itself, of particular importance and can be considered the secondary objective of this work. Satisfactory and promising results have been obtained in this second goal.
Epidemic modeling is an essential tool to understand the spread of the novel coronavirus and ultimately assist in disease prevention, policymaking, and resource allocation. In this article, we establish a state of the art interface between classic mathematical and statistical models and propose a novel space-time epidemic modeling framework to study the spatial-temporal pattern in the spread of infectious disease. We propose a quasi-likelihood approach via the penalized spline approximation and alternatively reweighted least-squares technique to estimate the model. Furthermore, we provide a sh…
Since December 2019, the world has been witnessing the gigantic effect of an unprecedented global pandemic called Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) - COVID-19. So far, 38,619,674 confirmed cases and 1,093,522 confirmed deaths due to COVID-19 have been reported. In the United States (US), the cases and deaths are recorded as 7,833,851 and 215,199. Several timely researches have discussed the local and global effects of the confounding factors on COVID-19 casualties in the US. However, most of these studies considered little about the time varying associations between an…
With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper we approach the forecasting task with an alternative technique - spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a Long Short-term M…
Most COVID-19 predictive modeling efforts use statistical or mathematical models to predict national- and state-level COVID-19 cases or deaths in the future. These approaches assume parameters such as reproduction time, test positivity rate, hospitalization rate, and social intervention effectiveness (masking, distancing, and mobility) are constant. However, the one certainty with the COVID-19 pandemic is that these parameters change over time, as well as vary across counties and states. In fact, the rate of spread over region, hospitalization rate, hospital length of stay and mortality rate, …
The outbreaks of Coronavirus Disease 2019 (COVID-19) have impacted the world significantly. Modeling the trend of infection and real-time forecasting of cases can help decision making and control of the disease spread. However, data-driven methods such as recurrent neural networks (RNN) can perform poorly due to limited daily samples in time. In this work, we develop an integrated spatiotemporal model based on the epidemic differential equations (SIR) and RNN. The former after simplification and discretization is a compact model of temporal infection trend of a region while the latter models t…
In March 2020 the United Kingdom (UK) entered a nationwide lockdown period due to the Covid-19 pandemic. As a result, levels of nitrogen dioxide (NO2) in the atmosphere dropped. In this work, we use 550,134 NO2 data points from 237 stations in the UK to build a spatiotemporal Gaussian process capable of predicting NO2 levels across the entire UK. We integrate several covariate datasets to enhance the model's ability to capture the complex spatiotemporal dynamics of NO2. Our numerical analyses show that, within two weeks of a UK lockdown being imposed, UK NO2 levels dropped 36.8%. Further, we s…
Currently, Brazil has one of the fastest increasing COVID-19 epidemics in the world, that has caused at least 94 thousand confirmed deaths until now. The city of Sao Paulo is particularly vulnerable because it is the most populous in the country. Analyzing the spatiotemporal dynamics of COVID-19 is important to help the urgent need to integrate better actions to face the pandemic. Thus, this study aimed to analyze the COVID-19 mortality, from March to July 2020, considering the spatio-time architectures, the socio-economic context of the population, and using a fine granular level, in the most…
We compare two multi-state modelling frameworks that can be used to represent dates of events following hospital admission for people infected during an epidemic. The methods are applied to data from people admitted to hospital with COVID-19, to estimate the probability of admission to ICU, the probability of death in hospital for patients before and after ICU admission, the lengths of stay in hospital, and how all these vary with age and gender. One modelling framework is based on defining transition-specific hazard functions for competing risks. A less commonly used framework defines partial…
Potential Landscapes Reveal Spatiotemporal Structure in Urban Mobility: Hodge Decomposition and Principal Component Analysis of Tokyo Before and During COVID-19
Diagnosing glaucoma progression is critical for limiting irreversible vision loss. A common method for assessing glaucoma progression uses a longitudinal series of visual fields (VF) acquired at regular intervals. VF data are characterized by a complex spatiotemporal structure due to the data generating process and ocular anatomy. Thus, advanced statistical methods are needed to make clinical determinations regarding progression status. We introduce a spatiotemporal boundary detection model that allows the underlying anatomy of the optic disc to dictate the spatial structure of the VF data acr…
The statistical methods used to analyze medical data are becoming increasingly complex. Novel statistical methods increasingly rely on simulation studies to assess their validity. Such assessments typically appear in statistical or computational journals, and the methodology is later introduced to the medical community through tutorials. This can be problematic if applied researchers use the methodologies in settings that have not been evaluated. In this paper, we explore a case study of one such method that has become popular in the analysis of coronavirus disease 2019 (COVID-19) data. The in…
This article describes a new method for estimating weekly incidence (new onset) of symptoms consistent with Influenza and COVID-19, using data from the Flutracking survey. The method mitigates some of the known self-selection and symptom-reporting biases present in existing approaches to this type of participatory longitudinal survey data. The key novel steps in the analysis are: 1) Identifying new onset of symptoms for three different Symptom Groupings: COVID-like illness (CLI1+, CLI2+), and Influenza-like illness (ILI), for responses reported in the Flutracking survey. 2) Adjusting for sympt…
The outbreak of Coronavirus Disease 2019 (COVID-19) is an ongoing pandemic affecting over 200 countries and regions. Inference about the transmission dynamics of COVID-19 can provide important insights into the speed of disease spread and the effects of mitigation policies. We develop a novel Bayesian approach to such inference based on a probabilistic compartmental model using data of daily confirmed COVID-19 cases. In particular, we consider a probabilistic extension of the classical susceptible-infectious-recovered model, which takes into account undocumented infections and allows the epide…
University of New South Wales（新南威尔士大学）；Indian Institute of Technology Guwahati（印度理工学院古瓦哈提分校）
The COVID-19 pandemic continues to have major impact to health and medical infrastructure, economy, and agriculture. Prominent computational and mathematical models have been unreliable due to the complexity of the spread of infections. Moreover, lack of data collection and reporting makes modelling attempts difficult and unreliable. Hence, we need to re-look at the situation with reliable data sources and innovative forecasting models. Deep learning models such as recurrent neural networks are well suited for modelling spatiotemporal sequences. In this paper, we apply recurrent neural network…
As the COVID-19 outbreak is developing the two most frequently reported statistics seem to be the raw confirmed case and case fatalities counts. Focusing on Italy, one of the hardest hit countries, we look at how these two values could be put in perspective to reflect the dynamics of the virus spread. In particular, we find that merely considering the confirmed case counts would be very misleading. The number of daily tests grows, while the daily fraction of confirmed cases to total tests has a change point. It (depending on region) generally increases with strong fluctuations till (around, de…
Machine Learning and ARIMA Model Averaging for Adaptive Public Health Forecasting: Comparative Evaluation and an Ontario COVID-19 Case Study
Public Health Ontario（安大略省公共卫生局）；Dalla Lana School of Public Health, University of Toronto（多伦多大学达拉·拉纳公共卫生学院）；University of Toronto（多伦多大学）；York University（约克大学）
