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COVID-19 Risk Estimation using a Time-varying SIR-model [article]

Mehrdad Kiamari, Gowri Ramachandran, Quynh Nguyen, Eva Pereira, Jeanne Holm, Bhaskar Krishnamachari
2020 arXiv   pre-print
We propose a rigorous hybrid model-and-data-driven approach to risk scoring based on a time-varying SIR epidemic model that ultimately yields a simplified color-coded risk level for each community.  ...  We show how this risk score can be estimated using another useful metric of infection spread, R_t, the time-varying average reproduction number which indicates the average number of individuals an infected  ...  We show how this can be estimated using a time-varying SIR model, a generalization of the well-known SIR compartmental model [4] , [5] which consists of three states, namely the susceptible state, the  ... 
arXiv:2008.08140v1 fatcat:vtftbwvkonccln7qz7o3ucbubq

Discussion of "Evaluate the Risk of Resumption of Business for the States of New York, New Jersey and Connecticut via a Pre-Symptomatic and Asymptomatic Transmission Model of COVID-19"

Yishu Xue, Hou-Cheng Yang, Yuqing Pan, Guanyu Hu
2021 Journal of Data Science  
Many variants of the SIR model or its extensions have been used to model the development of COVID-19 from different aspects (see, Wang et al., 2020; Yang et al., 2020; Hu and Geng, 2020 ).  ...  The Proposed SIHC Model There is a notable amount of work done by statisticians and biostatisticians since the breakout of COVID-19.  ...  Many variants of the SIR model or its extensions have been used to model the development of COVID-19 from different aspects (see, Wang et al., 2020; Yang et al., 2020; Hu and Geng, 2020 ).  ... 
doi:10.6339/21-jds994c fatcat:reitpbqgxjcftjn6g7cmh4tc4u

Discussion of "Evaluate the Risk of Resumption of Business for the States of New York, New Jersey and Connecticut via a Pre-Symptomatic and Asymptomatic Transmission Model of COVID-19"

Chuanrong Zhang, Xinba Li
2021 Journal of Data Science  
the risk of reopening business via a pre-symptomatic and asymptomatic transmission model of COVID-19.  ...  Tian et al. (2021) makes a timely contribution to provide predicted COVID-19 risk information for the policy-makers to evaluate their reopening plans.  ... 
doi:10.6339/21-jds994e fatcat:4uwgtxwezjeingg6cz66knutky

Estimating individual risks of COVID-19-associated hospitalization and death using publicly available data

Rajiv Bhatia, Jeffrey Klausner, Jeffrey Shaman
2020 PLoS ONE  
Using the method, we estimate that risks for a 90-day period at the median daily summertime U.S. county confirmed COVID-19 case incidence of 10.8 per 100,000 and pre-pandemic contact rates range from 0.4  ...  These estimates are sensitive to the parameter assumptions; nevertheless, they are comparable to the COVID-19 hospitalization and fatality rates observed over the time period.  ...  Estimated risk of death and hospitalization at pre-pandemic U.S. contact rates over a 90-day time period at the median county incidence of confirmed infections during the "summer wave' of the COVID-19  ... 
doi:10.1371/journal.pone.0243026 pmid:33284861 fatcat:vmumslc3cfemlnlnr5dmzg6dmu

Cure and death play a role in understanding dynamics for COVID-19: Data-driven competing risk compartmental models, with and without vaccination

Min Lu, Hemant Ishwaran, Yury E Khudyakov
2021 PLoS ONE  
Several factors have played a strong role in influencing the dynamics of COVID-19 in the U.S.  ...  Computations are performed using a simple discrete time algorithm that utilizes a data driven contact rate.  ...  Extensions to the basic SIR model to include other stages have been considered for COVID-19 [18] [19] [20] [21] [22] .  ... 
doi:10.1371/journal.pone.0254397 fatcat:3vatncsfa5aofl5rqgdnehfna4

Estimating Unreported COVID-19 Cases with a Time-Varying SIR Regression Model

Zhenghong Peng, Siya Ao, Lingbo Liu, Shuming Bao, Tao Hu, Hao Wu, Ru Wang
2021 International Journal of Environmental Research and Public Health  
We suggested taking time-varying Susceptible-Infected-Recovered (SIR) models with unreported infection rates (UIR) to estimate factual COVID-19 cases in the United States.  ...  Methods: Both the SIR model integrated with unreported infection rates (SIRu) of fixed-time effect and SIRu with time-varying parameters (tvSIRu) were applied to estimate and compare the values of transmission  ...  A recent study suggested using a time-varying SIR model to capture the changing transmissive rate [21] .  ... 
doi:10.3390/ijerph18031090 pmid:33530563 pmcid:PMC7908085 fatcat:o64cvqnzxngodkduceeb4csxlm

Are we there yet? Adaptive SIR model for continuous estimation of COVID-19 infection rate and reproduction number in the United States (Preprint)

Mark Shapiro, Fazle Karim, Guido Muscioni, Abel Saju Augustine
2020 Journal of Medical Internet Research  
We propose a simple method for estimating the time-varying infection rate and reproduction number R_t . We use a sliding window approach applied to a Susceptible-Infectious-Removed model.  ...  The dynamics of the COVID-19 epidemic vary due to local population density and policy measures.  ...  Discussion Principal Findings We developed a simple approach to adaptively estimate the time-varying parameters of the SIR model, using reported data on the number of confirmed COVID-19 cases.  ... 
doi:10.2196/24389 pmid:33755577 fatcat:zyfoajzftnedjeckjft7tbocwy

Scaling analysis of COVID-19 spreading based on Belgian hospitalization data [article]

Bart Smeets, Rodrigo Watte, Herman Ramon
2020 medRxiv   pre-print
Based on the SIR-X model fit, we analyze the COVID-19 mortality and the number of patients requiring ICU treatment over time.  ...  For the latter, we estimate a power law exponent of ≈ 2.2, which is consistent with growth kinetics of COVID-19 in China and indicative of the underlying small world network structure of the epidemic.  ...  When extrapolating the number of deaths using the SIR-X model, the predicted death toll due to COVID-19 will exceed 10 3 by April 3rd.  ... 
doi:10.1101/2020.03.29.20046730 fatcat:gams7fqpgng7vepbfh5hvsumia

An epidemiological forecast model and software assessing interventions on the COVID-19 epidemic in China

Lili Wang, Yiwang Zhou, Jie He, Bin Zhu, Fei Wang, Lu Tang, Michael Kleinsasser, Daniel Barker, Marisa C. Eisenberg, Peter X.K. Song
2021 Journal of Data Science  
As a case study, we examine the novel coronavirus (COVID-19) epidemic using the publicly available data from the China CDC.  ...  We extend the SIR model to incorporate various types of time-varying quarantine protocols, including government-level 'macro' isolation policies and community-level 'micro' social distancing (e.g. self-isolation  ...  Figure 1 : 1 A conceptual framework of the proposed epidemiological state-space SIR model. at time t: Figure 2 : 2 Extended SIR models with a time-varying transmission rate modifier π(t) (Panel A) or  ... 
doi:10.6339/jds.202007_18(3).0003 fatcat:nw2syewsfvfdbk7g6uh3bwntba

COVID-19 Fatality: A Cross-Sectional Study using Adaptive Lasso Penalized Sliced Inverse Regression

Kaida Cai, Wenqing He, Grace Y. Yi
2021 Journal of Data Science  
We apply the proposed method to conduct a cross-sectional study for the COVID-19 data obtained from two time points of the outbreak.  ...  We employ a multiple index model in combination with sliced inverse regression to facilitate the relationship between the IFR and possible risk factors.  ...  This research is partially supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) as well as the Rapid Response Program -COVID-19 of the Canadian Statistical Sciences Institute  ... 
doi:10.6339/jds.202007_18(3).0015 fatcat:ggqatm2w6vgtllg7hoj356g4zu

Rejoinder: An epidemiological forecast model and software assessing interventions on COVID-19 epidemic in China

Lili Wang, Yiwang Zhou, Jie He, Bin Zhu, Fei Wang, Lu Tang, Michael Kleinsasser, Daniel Barker, Marisa C. Eisenberg, Peter X.K. Song
2021 Journal of Data Science  
day ahead risk prediction of COVID-19 for each county in state Maryland from May 2, 2020.  ...  Our recent project proposed a spatiotemporal epidemiological forecast model that combines a spatial cellular automata (CA) with the eSAIR model (1) to predict the infection risk of COVID-19 for 3109 counties  ... 
doi:10.6339/jds.202007_18(3).0009 fatcat:mcccxjv6l5hobicpnz42armzkm

Risk of a second wave of Covid-19 infections: using artificial intelligence to investigate stringency of physical distancing policies in North America

Shashank Vaid, Aaron McAdie, Ran Kremer, Vikas Khanduja, Mohit Bhandari
2020 International Orthopaedics  
Moreover, there is a need for a multidimensional county-level approach to monitor the second wave of covid-19 in the USA.  ...  Accurately forecasting the occurrence of future covid-19-related cases across relaxed (Sweden) and stringent (USA and Canada) policy contexts has a renewed sense of urgency.  ...  Fig Fig. 4 a (Clockwise) Effective growth rate of covid-19 cases for Sweden; Bayesian SIR model forecast of new confirmed covid-19 cases for Sweden; and Number of new covid-19 cases in Sweden. b Kalman  ... 
doi:10.1007/s00264-020-04653-3 pmid:32504213 pmcid:PMC7411331 fatcat:wjrh52w5evavrandhyeudvugja

COVID-19 and output in Japan

Daisuke Fujii, Taisuke Nakata
2021 Japanese Economic Review  
AbstractWe build a tractable SIR-macro-model with time-varying parameters and use it to explore various policy questions such as when to lift the state of emergency (SOE).  ...  Our model-based analysis—updated weekly since January 2021, frequently reported by media, and presented to policymakers on many occasions—has played a unique role in the policy response to the COVID-19  ...  We build a tractable SIR-macro-model with time-varying parameters and quantify the relationship between the spread of COVID-19 and output in Japan.  ... 
doi:10.1007/s42973-021-00098-4 pmid:34566466 pmcid:PMC8455238 fatcat:b3lydbljpjdi5nub23x7x66lyi

Discussion on "The timing and effectiveness of implementing mild interventions of COVID-19 in large industrial regions via a synthetic control method" by Tian et al

Debashree Ray, Rupam Bhattacharyya, Bhramar Mukherjee
2021 Statistics and its Interface  
used in recent works on SIR-type models of COVID-19 (Ray et al., 2020) .  ...  Given that the model inherently relies upon a time-varying reproduction number (which can be calculated based on the estimated parameters), it would be interesting to look at this quantity over time as  ... 
doi:10.4310/20-sii653 fatcat:imdm2byqsvhmtbiekhawv3pd7i

Household Transmission of SARS-CoV-2, Zhuhai, China, 2020

Jian Wu, Yiying Huang, Changli Tu, Chunping Bi, Zhigang Chen, Liyun Luo, Mingxing Huang, Meizhu Chen, Cuiyan Tan, Zhenguo Wang, Kongqiu Wang, YingJian Liang (+3 others)
2020 Clinical Infectious Diseases  
To illustrate the extent of transmission, identify affecting risk factors and estimate epidemiological modeling parameters of SARS-CoV-2 in household setting.  ...  Early isolation of patients with COVID-19 and prioritizing rapid contact investigation, followed by active symptom monitoring and periodic laboratory evaluation, should be initiated immediately after confirming  ...  increased risk for COVID-19, respectively.  ... 
doi:10.1093/cid/ciaa557 pmid:32392331 fatcat:o46h2arkg5h6bnmu62ciqtqrpy
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