|
covidseir Resource1 #686691 covidseir fits a Bayesian SEIR (Susceptible, Exposed, Infectious, Recovered) model to daily COVID-19 case data. The package focuses on estimating the fraction of the usual contact rate for individuals participating in physical distancing (social distancing). The model is coded in Stan. The model can accommodate multiple types of case data at once (e.g., reported cases, hospitalizations, ICU admissions) and accounts for delays between symptom onset and case appearance. [1] | |
+Citations (4) - CitationsAdd new citationList by: CiterankMapLink[2] Interactive Social Distance Modelling
Cited by: David Price 3:34 PM 14 September 2022 GMT URL: | Excerpt / Summary About the Model: In this very simple model of social distancing, a fixed portion of the population is willing or able to follow distancing, and for those who are, all contacts are reduced by a fraction f. This simple model agrees well with more complex models that consider different kinds of contacts (home, work, school, community) with opposing effects under different kinds of social distancing measures. For example, with schools closed, household contact rates may have a slight rise; some community contacts remain even if people work remotely. This model assumes homogeneous mixing in the population, which despite the complexity of human communities, has been shown to do a surprisingly good job of reflecting the dynamics of respiratory viruses. This model has the advantage that it does not require detailed information about age and contact rates and the simulation and code are simple.
Limitations: This model does not have age or contact structure and assumes that the population mixes evenly. We have made guesses about the fraction of contacts that different kinds of activities might represent. These are loosely based on the Imperial College London Report 13, at https://www.imperial.a..., workplaces, schools and communities. However it is not known what fraction of the COVID-19 transmission opportunities arise through different activities, nor how different age groups contribute to transmission. This model does not explicitly include individuals who may be infectious but never show symptoms. Parameter values are always uncertain (within reason) in any model. |
Link[3] Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing
Author: Sean C. Anderson, Andrew M. Edwards, Madi Yerlanov, Nicola Mulberry, Jessica E. Stockdale, Sarafa A. Iyaniwura, Rebeca C. Falcao, Michael C. Otterstatter, Michael A. Irvine, Naveed Z. Janjua, Daniel Coombs, Caroline Colijn Publication date: 3 December 2020 Publication info: PLoS Comput Biol 16(12): e1008274 Cited by: David Price 3:39 PM 14 September 2022 GMT Citerank: (2) 690180British Columbia COVID-19 GroupThe BC COVID-19 Modelling Group works on rapid response modelling of the COVID-19 pandemic, with a special focus on British Columbia and Canada.10015D3D3AB, 714608Charting a FutureCharting a Future for Emerging Infectious Disease Modelling in Canada – April 2023 [1] 2794CAE1 URL: DOI: https://doi.org/10.1371/journal.pcbi.1008274
| Excerpt / Summary Extensive non-pharmaceutical and physical distancing measures are currently the primary interventions against coronavirus disease 2019 (COVID-19) worldwide. It is therefore urgent to estimate the impact such measures are having. We introduce a Bayesian epidemiological model in which a proportion of individuals are willing and able to participate in distancing, with the timing of distancing measures informed by survey data on attitudes to distancing and COVID-19. We fit our model to reported COVID-19 cases in British Columbia (BC), Canada, and five other jurisdictions, using an observation model that accounts for both underestimation and the delay between symptom onset and reporting. We estimated the impact that physical distancing (social distancing) has had on the contact rate and examined the projected impact of relaxing distancing measures. We found that, as of April 11 2020, distancing had a strong impact in BC, consistent with declines in reported cases and in hospitalization and intensive care unit numbers; individuals practising physical distancing experienced approximately 0.22 (0.11–0.34 90% CI [credible interval]) of their normal contact rate. The threshold above which prevalence was expected to grow was 0.55. We define the “contact ratio” to be the ratio of the estimated contact rate to the threshold rate at which cases are expected to grow; we estimated this contact ratio to be 0.40 (0.19–0.60) in BC. We developed an R package ‘covidseir’ to make our model available, and used it to quantify the impact of distancing in five additional jurisdictions. As of May 7, 2020, we estimated that New Zealand was well below its threshold value (contact ratio of 0.22 [0.11–0.34]), New York (0.60 [0.43–0.74]), Washington (0.84 [0.79–0.90]) and Florida (0.86 [0.76–0.96]) were progressively closer to theirs yet still below, but California (1.15 [1.07–1.23]) was above its threshold overall, with cases still rising. Accordingly, we found that BC, New Zealand, and New York may have had more room to relax distancing measures than the other jurisdictions, though this would need to be done cautiously and with total case volumes in mind. Our projections indicate that intermittent distancing measures—if sufficiently strong and robustly followed—could control COVID-19 transmission. This approach provides a useful tool for jurisdictions to monitor and assess current levels of distancing relative to their threshold, which will continue to be essential through subsequent waves of this pandemic. |
Link[4] How much leeway is there to relax COVID-19 control measures?
Author: Sean C. Anderson, Nicola Mulberry, Andrew M. Edwards, Jessica E. Stockdale, Sarafa A. Iyaniwura, Rebeca C. Falcao, Michael C. Otterstatter, Naveed Z. Janjua, Daniel Coombs, Caroline Colijn Publication date: 7 May 2021 Publication info: Epidemics, Volume 35, June 2021, 100453, ISSN 1755-4365 Cited by: David Price 3:39 PM 14 September 2022 GMT Citerank: (1) 690180British Columbia COVID-19 GroupThe BC COVID-19 Modelling Group works on rapid response modelling of the COVID-19 pandemic, with a special focus on British Columbia and Canada.10015D3D3AB URL: DOI: https://doi.org/10.1016/j.epidem.2021.100453
| Excerpt / Summary Following successful non-pharmaceutical interventions (NPI) aiming to control COVID-19, many jurisdictions reopened their economies and borders. As little immunity had developed in most populations, re-establishing higher contact carried substantial risks, and therefore many locations began to see resurgence in COVID-19 cases. We present a Bayesian method to estimate the leeway to reopen, or alternatively the strength of change required to re-establish COVID-19 control, in a range of jurisdictions experiencing different COVID-19 epidemics. We estimated the timing and strength of initial control measures such as widespread distancing and compared the leeway jurisdictions had to reopen immediately after NPI measures to later estimates of leeway. Finally, we quantified risks associated with reopening and the likely burden of new cases due to introductions from other jurisdictions. We found widely varying leeway to reopen. After initial NPI measures took effect, some jurisdictions had substantial leeway (e.g., Japan, New Zealand, Germany) with > 0.99 probability that contact rates were below 80% of the threshold for epidemic growth. Others had little leeway (e.g., the United Kingdom, Washington State) and some had none (e.g., Sweden, California). For most such regions, increases in contact rate of 1.5–2 fold would have had high (> 0.7) probability of exceeding past peak sizes. Most jurisdictions experienced June–August trajectories consistent with our projections of contact rate increases of 1–2-fold. Under such relaxation scenarios for some regions, we projected up to ∼100 additional cases if just one case were imported per week over six weeks, even between jurisdictions with comparable COVID-19 risk. We provide an R package covidseir to enable jurisdictions to estimate leeway and forecast cases under different future contact patterns. Estimates of leeway can establish a quantitative basis for decisions about reopening. We recommend a cautious approach to reopening economies and borders, coupled with strong monitoring for changes in transmission. |
|
|