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Short term prediction
Row
Hospital Admissions
style(p[[4]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
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Mortality
style(p[[8]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
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Row
Hospital Admissions (cumulative)
style(p[[2]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
## Warning in normalizePath(f2): path[1]="webshot634f3e764847.png": No such file or directory
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Mortality (cumulative)
style(p[[6]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
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Long term prediction
Row
Hospital Admissions
style(p[[3]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
## Warning in normalizePath(f2): path[1]="webshot634f4dd0727f.png": No such file or directory
## Warning in file(con, "rb"): cannot open file 'webshot634f4dd0727f.png': No such file or ## directory
## Error in file(con, "rb"): cannot open the connection
Mortality
style(p[[7]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
## Warning in normalizePath(f2): path[1]="webshot634f670c40de.png": No such file or directory
## Warning in file(con, "rb"): cannot open file 'webshot634f670c40de.png': No such file or ## directory
## Error in file(con, "rb"): cannot open the connection
Row
Hospital Admissions (cumulative)
style(p[[1]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
## Warning in normalizePath(f2): path[1]="webshot634f53465aef.png": No such file or directory
## Warning in file(con, "rb"): cannot open file 'webshot634f53465aef.png': No such file or ## directory
## Error in file(con, "rb"): cannot open the connection
Mortality (cumulative)
style(p[[5]], showlegend = FALSE)
## PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
## Warning in normalizePath(f2): path[1]="webshot634fcfac9d1.png": No such file or directory
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Readme
Update 2020-05-19
The model used in this case is the one proposed in Hauser et al. (2020), but adapted to the estimation of mortality and hospital admissions in the Basque Country. As indicated in the paper by Althaus et al. (2020) ( referred to the reader for more details), this is an SEIR (Susceptible-Exposed-Infected-Recovered) model stratified by age, with a distinction between symptomatic and asymptomatic infections. The population is divided into nine age groups (0-9 years, 10-19 years,\(\ldots\) , 70-79 years, over 80 years).
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The population of each \(k\) age group is subdivided into five compartments: susceptible (\(S_k\)), incubating or exposed (\(E_k\)), infected with symptoms (\(I_k\)), infected and asymptomatic (\(A_k\)), and recovered and dead (\(R_k\)) (see Figure \ref{fig1_annex_SEIR}).
The number of individuals in each compartment is scaled according to the total population of the Basque Country (2,188,017 inhabitants in 2019), so that the sum of all compartments is 1.
References
- Hauser A, Counotte MJ, Margossian CC, Konstantinoudis G, Low N, Althaus CL, Riou J.
Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: a modelling study in Hubei, China and northern Italy. \textit{medRxiv} 2020 (DOI: https://doi.org/10.1101/2020.03.04.20031104).
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